Starting phenix.real_space_refine on Tue Sep 24 11:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/09_2024/6ruo_10007.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/09_2024/6ruo_10007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/09_2024/6ruo_10007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/09_2024/6ruo_10007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/09_2024/6ruo_10007.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/09_2024/6ruo_10007.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 92 5.49 5 S 236 5.16 5 C 31988 2.51 5 N 8763 2.21 5 O 9705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50792 Number of models: 1 Model: "" Number of chains: 26 Chain: "Q" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3572 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 11567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1465, 11567 Classifications: {'peptide': 1465} Link IDs: {'PTRANS': 59, 'TRANS': 1405} Chain breaks: 7 Chain: "B" Number of atoms: 9371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9371 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3807 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "T" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1000 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "U" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 901 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4867 SG CYS A 62 90.882 68.643 55.402 1.00206.29 S ATOM 4886 SG CYS A 65 89.578 65.457 57.326 1.00205.70 S ATOM 5212 SG CYS A 105 134.340 48.337 75.164 1.00154.29 S ATOM 6011 SG CYS A 233 135.160 47.348 78.508 1.00161.07 S ATOM 6033 SG CYS A 236 138.325 48.700 76.465 1.00166.28 S ATOM 24674 SG CYS B1107 96.660 52.213 61.717 1.00158.67 S ATOM 33644 SG CYS I 13 143.904 105.020 128.253 1.00115.67 S ATOM 33764 SG CYS I 30 145.997 103.005 126.084 1.00123.44 S ATOM 34192 SG CYS I 86 76.281 54.749 130.493 1.00225.37 S ATOM 34214 SG CYS I 89 77.100 52.066 133.433 1.00242.90 S ATOM 34431 SG CYS I 117 80.251 53.517 130.865 1.00251.09 S ATOM 34555 SG CYS J 7 49.375 96.408 110.539 1.00 70.94 S ATOM 34578 SG CYS J 10 45.423 95.930 110.617 1.00 66.58 S ATOM 34858 SG CYS J 45 48.117 94.746 113.566 1.00 69.06 S ATOM 34864 SG CYS J 46 46.232 98.565 113.791 1.00 72.08 S ATOM 35930 SG CYS L 31 73.782 121.659 83.281 1.00 76.67 S ATOM 35950 SG CYS L 34 72.689 125.018 84.119 1.00 80.79 S ATOM 36054 SG CYS L 48 73.546 123.447 80.102 1.00 77.73 S ATOM 36077 SG CYS L 51 76.187 124.354 83.963 1.00 71.94 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 20.32, per 1000 atoms: 0.40 Number of scatterers: 50792 At special positions: 0 Unit cell: (166.32, 215.16, 174.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 236 16.00 P 92 15.00 O 9705 8.00 N 8763 7.00 C 31988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.12 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 117 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 12 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11548 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 65 sheets defined 35.8% alpha, 10.7% beta 11 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 12.79 Creating SS restraints... Processing helix chain 'Q' and resid 100 through 122 removed outlier: 3.819A pdb=" N SER Q 107 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 112 " --> pdb=" O PHE Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 147 removed outlier: 3.969A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE Q 136 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE Q 140 " --> pdb=" O ILE Q 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU Q 141 " --> pdb=" O TRP Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 172 removed outlier: 3.580A pdb=" N THR Q 161 " --> pdb=" O HIS Q 157 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE Q 162 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 183 Processing helix chain 'Q' and resid 208 through 216 removed outlier: 3.559A pdb=" N ILE Q 214 " --> pdb=" O TYR Q 210 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU Q 216 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 237 removed outlier: 3.562A pdb=" N LYS Q 229 " --> pdb=" O GLN Q 225 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE Q 230 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 261 removed outlier: 3.570A pdb=" N LEU Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS Q 255 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU Q 256 " --> pdb=" O LEU Q 252 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 4.015A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS Q 271 " --> pdb=" O TYR Q 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.942A pdb=" N LEU Q 307 " --> pdb=" O GLU Q 303 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE Q 314 " --> pdb=" O PHE Q 310 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 332 Processing helix chain 'Q' and resid 334 through 339 Processing helix chain 'Q' and resid 344 through 357 removed outlier: 3.519A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL Q 355 " --> pdb=" O ASN Q 351 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 369 Processing helix chain 'Q' and resid 372 through 386 removed outlier: 3.896A pdb=" N GLU Q 376 " --> pdb=" O GLU Q 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Q 378 " --> pdb=" O THR Q 374 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS Q 383 " --> pdb=" O LYS Q 379 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 384 " --> pdb=" O TRP Q 380 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE Q 385 " --> pdb=" O MET Q 381 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU Q 386 " --> pdb=" O GLU Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 414 Processing helix chain 'Q' and resid 441 through 446 Processing helix chain 'Q' and resid 471 through 491 removed outlier: 3.531A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU Q 479 " --> pdb=" O ALA Q 475 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA Q 484 " --> pdb=" O LEU Q 480 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Q 488 " --> pdb=" O ALA Q 484 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP Q 490 " --> pdb=" O GLN Q 486 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE Q 491 " --> pdb=" O LEU Q 487 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 504 removed outlier: 3.700A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) Processing helix chain 'Q' and resid 505 through 514 removed outlier: 3.893A pdb=" N HIS Q 511 " --> pdb=" O ASN Q 507 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 512 " --> pdb=" O ALA Q 508 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET Q 513 " --> pdb=" O CYS Q 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.679A pdb=" N LEU A 54 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.588A pdb=" N TYR A 95 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.681A pdb=" N VAL A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.900A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.615A pdb=" N ASN A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.592A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 4.027A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.560A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 4.005A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.524A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.958A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.142A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.744A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 430 through 439 removed outlier: 3.629A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.920A pdb=" N VAL A 503 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.401A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.626A pdb=" N LYS A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.058A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.527A pdb=" N THR A 621 " --> pdb=" O HIS A 617 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.621A pdb=" N ALA A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.913A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.562A pdb=" N GLN A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.685A pdb=" N TRP A 760 " --> pdb=" O ASN A 757 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 761 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.958A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.990A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.737A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.511A pdb=" N LYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.019A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 912 removed outlier: 3.709A pdb=" N ILE A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.806A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1024 removed outlier: 4.183A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS A1022 " --> pdb=" O TYR A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1077 Processing helix chain 'A' and resid 1085 through 1089 removed outlier: 3.661A pdb=" N LEU A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1108 removed outlier: 3.533A pdb=" N THR A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1149 removed outlier: 3.948A pdb=" N LEU A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1177 Processing helix chain 'A' and resid 1186 through 1191 Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.509A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 removed outlier: 3.622A pdb=" N SER A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 3.759A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.735A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1326 Processing helix chain 'A' and resid 1326 through 1334 removed outlier: 4.251A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1454 Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.664A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.156A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1530 Processing helix chain 'A' and resid 1545 through 1553 removed outlier: 4.063A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.636A pdb=" N ASN A1560 " --> pdb=" O GLU A1556 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A1562 " --> pdb=" O ALA A1558 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.876A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.595A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.519A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A1626 " --> pdb=" O LEU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.677A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.306A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.586A pdb=" N ILE B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.923A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.557A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.501A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.502A pdb=" N LYS B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.545A pdb=" N GLY B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.363A pdb=" N GLY B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 4.081A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 404 through 424 removed outlier: 3.725A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 424 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 433 removed outlier: 4.052A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.556A pdb=" N SER B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.626A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 465 " --> pdb=" O MET B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 597 through 613 removed outlier: 3.626A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.767A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.883A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.883A pdb=" N HIS B 735 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.562A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 795 removed outlier: 3.578A pdb=" N ASP B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 removed outlier: 3.577A pdb=" N MET B 936 " --> pdb=" O THR B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.567A pdb=" N PHE B 954 " --> pdb=" O PRO B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.830A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.557A pdb=" N GLY B 997 " --> pdb=" O ALA B 993 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1083 removed outlier: 3.987A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY B1081 " --> pdb=" O ASP B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1093 removed outlier: 3.667A pdb=" N LEU B1093 " --> pdb=" O GLN B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1193 removed outlier: 3.626A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.683A pdb=" N PHE C 40 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.572A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.621A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.030A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.616A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.854A pdb=" N VAL C 255 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.855A pdb=" N GLU C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.536A pdb=" N ASN D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.655A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.907A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.401A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 27 removed outlier: 3.560A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.905A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.546A pdb=" N TYR E 46 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.866A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 104 removed outlier: 3.609A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.847A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 161 through 168 removed outlier: 3.796A pdb=" N TYR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'F' and resid 58 through 72 removed outlier: 5.193A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.821A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.758A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.514A pdb=" N VAL G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'J' and resid 14 through 18 removed outlier: 4.047A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 31 through 40 removed outlier: 4.146A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 removed outlier: 4.001A pdb=" N ARG J 48 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.558A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.783A pdb=" N ASN K 74 " --> pdb=" O HIS K 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 121 removed outlier: 3.784A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 133 removed outlier: 3.554A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'N' and resid 149 through 154 removed outlier: 4.219A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 60 removed outlier: 3.525A pdb=" N ALA O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 78 removed outlier: 4.598A pdb=" N ILE O 74 " --> pdb=" O GLN O 70 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 103 removed outlier: 3.893A pdb=" N LEU O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 112 No H-bonds generated for 'chain 'O' and resid 110 through 112' Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.732A pdb=" N SER O 118 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 3.522A pdb=" N SER O 134 " --> pdb=" O PRO O 130 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE O 147 " --> pdb=" O LEU O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.661A pdb=" N VAL O 154 " --> pdb=" O TRP O 150 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER O 155 " --> pdb=" O TRP O 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL O 159 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 178 removed outlier: 4.205A pdb=" N ASP O 174 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS O 177 " --> pdb=" O HIS O 173 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 4.463A pdb=" N LEU O 194 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.614A pdb=" N LYS O 207 " --> pdb=" O THR O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 217 removed outlier: 3.579A pdb=" N LEU O 215 " --> pdb=" O TYR O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 236 removed outlier: 3.757A pdb=" N SER O 231 " --> pdb=" O PHE O 227 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU O 233 " --> pdb=" O ILE O 229 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE O 234 " --> pdb=" O TRP O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 246 removed outlier: 4.370A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN O 245 " --> pdb=" O ASP O 241 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 334 removed outlier: 4.205A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 347 removed outlier: 3.881A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL O 339 " --> pdb=" O ILE O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 372 removed outlier: 3.910A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS O 369 " --> pdb=" O THR O 365 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR O 370 " --> pdb=" O THR O 366 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL O 372 " --> pdb=" O PHE O 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 removed outlier: 3.762A pdb=" N VAL O 388 " --> pdb=" O ILE O 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER O 389 " --> pdb=" O MET O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 408 removed outlier: 4.084A pdb=" N MET O 396 " --> pdb=" O GLN O 392 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER O 398 " --> pdb=" O GLU O 394 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL O 401 " --> pdb=" O ASP O 397 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR O 402 " --> pdb=" O SER O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 429 removed outlier: 3.730A pdb=" N GLY O 425 " --> pdb=" O LEU O 421 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 444 removed outlier: 3.735A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 450 Processing helix chain 'O' and resid 466 through 471 removed outlier: 4.228A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS O 471 " --> pdb=" O GLU O 468 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 485 removed outlier: 3.690A pdb=" N ALA O 476 " --> pdb=" O HIS O 472 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA O 479 " --> pdb=" O ALA O 475 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 509 removed outlier: 4.262A pdb=" N PHE O 506 " --> pdb=" O LEU O 502 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 522 through 535 removed outlier: 3.566A pdb=" N ARG O 530 " --> pdb=" O LEU O 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE O 531 " --> pdb=" O MET O 527 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA O 532 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU O 535 " --> pdb=" O ILE O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 545 Processing helix chain 'O' and resid 582 through 587 removed outlier: 3.714A pdb=" N ILE O 586 " --> pdb=" O ARG O 582 " (cutoff:3.500A) Processing helix chain 'O' and resid 601 through 605 Processing helix chain 'S' and resid 189 through 194 removed outlier: 3.954A pdb=" N ARG S 194 " --> pdb=" O ALA S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 576 removed outlier: 4.094A pdb=" N ALA S 575 " --> pdb=" O HIS S 571 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER S 576 " --> pdb=" O PRO S 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 571 through 576' Processing helix chain 'S' and resid 587 through 607 removed outlier: 4.210A pdb=" N LEU S 592 " --> pdb=" O SER S 588 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 596 " --> pdb=" O LEU S 592 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER S 605 " --> pdb=" O ARG S 601 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) Processing helix chain 'S' and resid 607 through 612 removed outlier: 3.646A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 617 through 644 removed outlier: 3.664A pdb=" N GLN S 624 " --> pdb=" O ASP S 620 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN S 635 " --> pdb=" O SER S 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU S 636 " --> pdb=" O ILE S 632 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU S 637 " --> pdb=" O ALA S 633 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.629A pdb=" N SER S 676 " --> pdb=" O ILE S 672 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER S 677 " --> pdb=" O PRO S 673 " (cutoff:3.500A) Processing helix chain 'S' and resid 700 through 705 removed outlier: 4.413A pdb=" N LEU S 704 " --> pdb=" O LEU S 700 " (cutoff:3.500A) Processing helix chain 'S' and resid 710 through 720 removed outlier: 4.261A pdb=" N TYR S 715 " --> pdb=" O LEU S 711 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN S 716 " --> pdb=" O ASP S 712 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS S 717 " --> pdb=" O ILE S 713 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU S 718 " --> pdb=" O PHE S 714 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 742 removed outlier: 3.832A pdb=" N GLU S 735 " --> pdb=" O LEU S 731 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE S 736 " --> pdb=" O LEU S 732 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL S 737 " --> pdb=" O THR S 733 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS S 738 " --> pdb=" O LYS S 734 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP S 739 " --> pdb=" O GLU S 735 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 766 removed outlier: 3.696A pdb=" N GLN S 757 " --> pdb=" O PHE S 753 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE S 760 " --> pdb=" O ILE S 756 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER S 761 " --> pdb=" O GLN S 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG S 762 " --> pdb=" O ASN S 758 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER S 763 " --> pdb=" O GLU S 759 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 removed outlier: 3.760A pdb=" N ARG R 17 " --> pdb=" O PHE R 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN R 22 " --> pdb=" O LYS R 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG R 33 " --> pdb=" O ARG R 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 34 " --> pdb=" O ARG R 30 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 130 removed outlier: 3.766A pdb=" N LYS R 129 " --> pdb=" O LYS R 126 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS R 130 " --> pdb=" O PHE R 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 126 through 130' Processing helix chain 'R' and resid 158 through 164 Processing helix chain 'R' and resid 166 through 173 Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.551A pdb=" N LEU R 177 " --> pdb=" O MET R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 removed outlier: 3.846A pdb=" N LEU R 186 " --> pdb=" O LYS R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 219 removed outlier: 3.744A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 225 Processing helix chain 'R' and resid 228 through 237 removed outlier: 4.445A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 253 removed outlier: 4.050A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 259 removed outlier: 3.877A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 removed outlier: 3.976A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR R 278 " --> pdb=" O MET R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 323 removed outlier: 3.642A pdb=" N SER R 316 " --> pdb=" O TYR R 312 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE R 318 " --> pdb=" O TRP R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 353 Processing helix chain 'R' and resid 362 through 379 removed outlier: 3.610A pdb=" N PHE R 366 " --> pdb=" O ALA R 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP R 377 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 421 removed outlier: 4.101A pdb=" N HIS R 407 " --> pdb=" O GLN R 403 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL R 411 " --> pdb=" O HIS R 407 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG R 412 " --> pdb=" O ILE R 408 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR R 413 " --> pdb=" O HIS R 409 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS R 421 " --> pdb=" O ILE R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 429 through 443 removed outlier: 3.816A pdb=" N ASN R 433 " --> pdb=" O ARG R 429 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER R 437 " --> pdb=" O ASN R 433 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE R 438 " --> pdb=" O GLN R 434 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 439 " --> pdb=" O LEU R 435 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER R 440 " --> pdb=" O LYS R 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 11 through 15 removed outlier: 3.978A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN M 82 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 23 through 25 removed outlier: 6.493A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'M' and resid 38 through 42 removed outlier: 3.679A pdb=" N GLU M 61 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL M 101 " --> pdb=" O GLU M 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 14 removed outlier: 7.006A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 86 removed outlier: 10.330A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 85 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.808A pdb=" N HIS A 107 " --> pdb=" O CYS A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.831A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.204A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 483 removed outlier: 5.845A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 507 through 510 removed outlier: 7.039A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB4, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.547A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS A 772 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.659A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 777 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 774 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 949 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.659A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 777 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB8, first strand: chain 'A' and resid 1238 through 1239 Processing sheet with id=AB9, first strand: chain 'A' and resid 1460 through 1462 removed outlier: 4.016A pdb=" N CYS A1470 " --> pdb=" O MET A1294 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A1269 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1272 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A1274 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 47 " --> pdb=" O GLU A1274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1506 through 1508 removed outlier: 3.952A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 73 through 74 removed outlier: 4.700A pdb=" N ASP F 145 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.268A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.979A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.662A pdb=" N LEU B 403 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 214 through 215 removed outlier: 5.395A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 259 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.825A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 592 through 596 removed outlier: 6.229A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 661 through 664 Processing sheet with id=AD1, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.817A pdb=" N ARG B 743 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 805 " --> pdb=" O TYR B 905 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 825 Processing sheet with id=AD3, first strand: chain 'B' and resid 857 through 859 removed outlier: 7.067A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.536A pdb=" N VAL B1103 " --> pdb=" O THR B1174 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD7, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.700A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.394A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.322A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE4, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.592A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.506A pdb=" N ASN E 63 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 108 through 112 removed outlier: 3.747A pdb=" N GLU E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.513A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 132 through 140 removed outlier: 7.404A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 6 removed outlier: 6.509A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 142 " --> pdb=" O MET H 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 16 removed outlier: 6.744A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 116 through 117 Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF5, first strand: chain 'I' and resid 81 through 83 Processing sheet with id=AF6, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AF7, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.971A pdb=" N LYS K 48 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 86 through 92 removed outlier: 6.247A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 80 through 81 removed outlier: 3.732A pdb=" N MET N 80 " --> pdb=" O TYR N 87 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 110 through 111 Processing sheet with id=AG2, first strand: chain 'S' and resid 25 through 26 removed outlier: 6.937A pdb=" N LEU S 25 " --> pdb=" O LYS S 439 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASP S 441 " --> pdb=" O LEU S 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE S 421 " --> pdb=" O SER S 418 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER S 418 " --> pdb=" O ILE S 421 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 63 through 67 removed outlier: 6.082A pdb=" N LEU S 64 " --> pdb=" O TYR S 549 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR S 549 " --> pdb=" O LEU S 64 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 182 through 183 removed outlier: 3.800A pdb=" N VAL S 213 " --> pdb=" O SER S 207 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AG6, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.419A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL S 261 " --> pdb=" O PHE S 272 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET S 285 " --> pdb=" O GLU S 275 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 300 through 303 removed outlier: 6.551A pdb=" N ASP S 319 " --> pdb=" O GLN S 301 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TRP S 324 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU S 347 " --> pdb=" O TRP S 324 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE S 326 " --> pdb=" O ASP S 345 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 362 through 365 removed outlier: 3.729A pdb=" N ARG S 362 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 449 through 457 removed outlier: 3.615A pdb=" N VAL S 465 " --> pdb=" O GLN S 454 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 478 through 479 Processing sheet with id=AH2, first strand: chain 'S' and resid 504 through 510 removed outlier: 6.578A pdb=" N LYS S 540 " --> pdb=" O THR S 506 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE S 508 " --> pdb=" O LEU S 538 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU S 538 " --> pdb=" O ILE S 508 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 19.47 Time building geometry restraints manager: 10.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13883 1.33 - 1.45: 10652 1.45 - 1.58: 26921 1.58 - 1.70: 181 1.70 - 1.82: 370 Bond restraints: 52007 Sorted by residual: bond pdb=" C THR A 659 " pdb=" N PRO A 660 " ideal model delta sigma weight residual 1.331 1.285 0.046 7.90e-03 1.60e+04 3.43e+01 bond pdb=" N MET Q 236 " pdb=" CA MET Q 236 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.20e-02 6.94e+03 1.22e+01 bond pdb=" N ILE O 237 " pdb=" CA ILE O 237 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N LEU Q 152 " pdb=" CA LEU Q 152 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.79e+00 bond pdb=" CA THR C 61 " pdb=" C THR C 61 " ideal model delta sigma weight residual 1.522 1.477 0.044 1.72e-02 3.38e+03 6.66e+00 ... (remaining 52002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 67576 2.28 - 4.56: 2625 4.56 - 6.84: 351 6.84 - 9.12: 89 9.12 - 11.40: 18 Bond angle restraints: 70659 Sorted by residual: angle pdb=" N ILE O 237 " pdb=" CA ILE O 237 " pdb=" C ILE O 237 " ideal model delta sigma weight residual 112.96 102.65 10.31 1.00e+00 1.00e+00 1.06e+02 angle pdb=" C LYS O 236 " pdb=" N ILE O 237 " pdb=" CA ILE O 237 " ideal model delta sigma weight residual 121.84 129.80 -7.96 1.13e+00 7.83e-01 4.97e+01 angle pdb=" C HIS S 230 " pdb=" N ASN S 231 " pdb=" CA ASN S 231 " ideal model delta sigma weight residual 122.46 130.59 -8.13 1.41e+00 5.03e-01 3.33e+01 angle pdb=" N ILE Q 281 " pdb=" CA ILE Q 281 " pdb=" C ILE Q 281 " ideal model delta sigma weight residual 110.62 116.92 -6.30 1.14e+00 7.69e-01 3.05e+01 angle pdb=" N ILE A1329 " pdb=" CA ILE A1329 " pdb=" C ILE A1329 " ideal model delta sigma weight residual 111.90 107.55 4.35 8.10e-01 1.52e+00 2.89e+01 ... (remaining 70654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 30775 35.28 - 70.56: 525 70.56 - 105.85: 39 105.85 - 141.13: 5 141.13 - 176.41: 6 Dihedral angle restraints: 31350 sinusoidal: 13543 harmonic: 17807 Sorted by residual: dihedral pdb=" CA GLU A 23 " pdb=" C GLU A 23 " pdb=" N ILE A 24 " pdb=" CA ILE A 24 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASP B 15 " pdb=" C ASP B 15 " pdb=" N PHE B 16 " pdb=" CA PHE B 16 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS B 894 " pdb=" C LYS B 894 " pdb=" N PHE B 895 " pdb=" CA PHE B 895 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 31347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 7282 0.104 - 0.207: 560 0.207 - 0.311: 25 0.311 - 0.415: 7 0.415 - 0.518: 4 Chirality restraints: 7878 Sorted by residual: chirality pdb=" CB ILE K 47 " pdb=" CA ILE K 47 " pdb=" CG1 ILE K 47 " pdb=" CG2 ILE K 47 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 7875 not shown) Planarity restraints: 8735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 659 " -0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO A 660 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 660 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 660 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 295 " 0.059 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO R 296 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO R 296 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 296 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 712 " 0.054 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 713 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 713 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 713 " 0.045 5.00e-02 4.00e+02 ... (remaining 8732 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2847 2.72 - 3.26: 48115 3.26 - 3.81: 82172 3.81 - 4.35: 102707 4.35 - 4.90: 167596 Nonbonded interactions: 403437 Sorted by model distance: nonbonded pdb=" O THR Q 12 " pdb="ZN ZN Q 601 " model vdw 2.170 2.230 nonbonded pdb=" O ASP Q 13 " pdb="ZN ZN Q 601 " model vdw 2.176 2.230 nonbonded pdb=" O THR Q 279 " pdb=" O ASP Q 280 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 618 " pdb=" O GLY B 780 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLU A 646 " pdb=" OG1 THR B1084 " model vdw 2.221 3.040 ... (remaining 403432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.560 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 101.380 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2898 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 52007 Z= 0.478 Angle : 1.048 11.404 70659 Z= 0.574 Chirality : 0.060 0.518 7878 Planarity : 0.007 0.087 8735 Dihedral : 13.248 176.412 19802 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.52 % Favored : 89.43 % Rotamer: Outliers : 0.40 % Allowed : 2.93 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.08), residues: 5986 helix: -4.09 (0.06), residues: 1897 sheet: -3.11 (0.18), residues: 646 loop : -2.95 (0.09), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP N 54 HIS 0.016 0.003 HIS B 183 PHE 0.042 0.003 PHE A 628 TYR 0.046 0.003 TYR R 368 ARG 0.020 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1324 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.4662 (ttp) cc_final: 0.2435 (mmp) REVERT: Q 209 ASN cc_start: 0.3140 (p0) cc_final: 0.2857 (p0) REVERT: Q 360 LYS cc_start: 0.4659 (ptpt) cc_final: 0.4311 (mmmt) REVERT: A 22 LYS cc_start: 0.6954 (mmpt) cc_final: 0.6315 (tmtt) REVERT: A 199 ASP cc_start: 0.5801 (m-30) cc_final: 0.5535 (m-30) REVERT: A 345 LEU cc_start: 0.2355 (mp) cc_final: 0.2070 (mp) REVERT: A 424 MET cc_start: 0.2821 (mmp) cc_final: 0.2235 (ppp) REVERT: A 458 GLN cc_start: 0.7224 (mm110) cc_final: 0.6715 (tm-30) REVERT: A 572 THR cc_start: 0.4483 (m) cc_final: 0.4262 (p) REVERT: A 758 GLU cc_start: 0.5581 (mp0) cc_final: 0.5379 (pt0) REVERT: A 1439 MET cc_start: 0.2096 (mtm) cc_final: 0.1059 (tpt) REVERT: A 1441 LYS cc_start: 0.5962 (tttm) cc_final: 0.5717 (mmtp) REVERT: A 1535 PHE cc_start: 0.4321 (m-80) cc_final: 0.4110 (m-10) REVERT: A 1620 GLN cc_start: 0.7380 (tp40) cc_final: 0.6552 (mp10) REVERT: A 1632 GLU cc_start: 0.4158 (tp30) cc_final: 0.3607 (tp30) REVERT: B 39 GLN cc_start: 0.4520 (mp10) cc_final: 0.4081 (mp10) REVERT: B 315 LYS cc_start: 0.7176 (tttm) cc_final: 0.6734 (mmtt) REVERT: B 358 VAL cc_start: 0.1022 (OUTLIER) cc_final: -0.0232 (p) REVERT: B 650 LEU cc_start: 0.1471 (mt) cc_final: 0.1169 (mt) REVERT: B 1097 ASP cc_start: 0.6892 (p0) cc_final: 0.6473 (p0) REVERT: E 65 THR cc_start: 0.4166 (p) cc_final: 0.3325 (t) REVERT: G 84 TYR cc_start: 0.4710 (p90) cc_final: 0.3499 (p90) REVERT: G 238 THR cc_start: 0.3496 (m) cc_final: 0.3084 (p) REVERT: G 241 ARG cc_start: 0.4199 (mtm-85) cc_final: 0.3873 (mpt180) REVERT: H 111 LEU cc_start: 0.5143 (mt) cc_final: 0.4914 (tp) REVERT: N 156 PRO cc_start: 0.5057 (Cg_endo) cc_final: 0.4844 (Cg_exo) REVERT: O 177 LYS cc_start: 0.6262 (ttpt) cc_final: 0.5456 (tptp) REVERT: O 218 LEU cc_start: 0.5515 (tp) cc_final: 0.4914 (tp) REVERT: O 229 ILE cc_start: 0.4194 (mm) cc_final: 0.3915 (pt) REVERT: O 385 MET cc_start: 0.2289 (tpp) cc_final: 0.1575 (tpt) REVERT: O 467 MET cc_start: 0.4521 (mmp) cc_final: 0.4005 (mmt) REVERT: O 608 GLU cc_start: 0.2948 (tm-30) cc_final: 0.2121 (pm20) REVERT: S 46 VAL cc_start: 0.1764 (p) cc_final: 0.1135 (p) REVERT: S 305 PHE cc_start: 0.5773 (m-10) cc_final: 0.5258 (t80) REVERT: S 323 ASN cc_start: 0.5467 (p0) cc_final: 0.4724 (p0) REVERT: S 344 ILE cc_start: 0.3913 (mm) cc_final: 0.3623 (pt) REVERT: S 389 TRP cc_start: 0.5553 (t60) cc_final: 0.2711 (t60) REVERT: S 416 LEU cc_start: 0.3392 (tp) cc_final: 0.3087 (tp) REVERT: S 622 TYR cc_start: 0.6568 (t80) cc_final: 0.6361 (t80) REVERT: S 639 GLU cc_start: 0.2003 (mm-30) cc_final: 0.1698 (mm-30) REVERT: S 730 GLU cc_start: 0.2301 (tp30) cc_final: 0.1686 (mm-30) REVERT: R 2 PHE cc_start: 0.3361 (m-80) cc_final: 0.2481 (m-10) REVERT: R 173 MET cc_start: 0.4863 (tpt) cc_final: 0.4633 (mmt) REVERT: R 297 PHE cc_start: 0.5046 (m-80) cc_final: 0.4713 (m-80) REVERT: R 401 ILE cc_start: 0.3353 (OUTLIER) cc_final: 0.2870 (tt) outliers start: 22 outliers final: 1 residues processed: 1340 average time/residue: 0.5493 time to fit residues: 1182.9747 Evaluate side-chains 637 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 634 time to evaluate : 4.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain R residue 401 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 515 optimal weight: 3.9990 chunk 463 optimal weight: 0.0980 chunk 256 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 478 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 356 optimal weight: 3.9990 chunk 554 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 33 HIS ** Q 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 238 HIS Q 283 ASN ** Q 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 435 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 264 ASN A 322 ASN A 332 GLN A 535 GLN A 560 GLN A 620 ASN A 706 HIS A 748 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 819 ASN A1026 GLN A1072 ASN A1088 HIS A1162 ASN A1180 ASN A1320 GLN A1447 GLN A1461 ASN A1487 ASN A1509 HIS A1568 ASN ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 62 ASN B 282 HIS B 361 HIS B 439 ASN B 492 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN B 735 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN B 952 HIS B1008 HIS B1041 ASN B1114 GLN B1165 ASN C 161 HIS C 172 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN G 20 HIS G 23 GLN G 26 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 128 GLN K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN N 106 ASN O 66 ASN O 94 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 391 GLN O 472 HIS S 346 ASN S 483 HIS S 665 ASN S 705 HIS R 207 ASN R 223 ASN ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 GLN R 286 GLN R 289 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 382 GLN R 407 HIS R 434 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3609 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 52007 Z= 0.266 Angle : 0.763 15.946 70659 Z= 0.403 Chirality : 0.046 0.298 7878 Planarity : 0.006 0.075 8735 Dihedral : 14.560 177.657 7615 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.52 % Allowed : 9.91 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.09), residues: 5986 helix: -3.08 (0.08), residues: 2047 sheet: -2.41 (0.19), residues: 662 loop : -2.56 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 380 HIS 0.013 0.001 HIS A 673 PHE 0.032 0.002 PHE B 313 TYR 0.035 0.002 TYR Q 446 ARG 0.014 0.001 ARG S 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 793 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.4091 (ttp) cc_final: 0.2036 (mmp) REVERT: Q 252 LEU cc_start: 0.3843 (OUTLIER) cc_final: 0.3532 (tt) REVERT: Q 317 MET cc_start: 0.5713 (mmt) cc_final: 0.5078 (tpt) REVERT: Q 360 LYS cc_start: 0.5238 (ptpt) cc_final: 0.4933 (mmmt) REVERT: M 30 PHE cc_start: 0.3564 (t80) cc_final: 0.2300 (t80) REVERT: A 80 GLU cc_start: 0.6201 (mm-30) cc_final: 0.4863 (tm-30) REVERT: A 199 ASP cc_start: 0.5985 (m-30) cc_final: 0.5420 (m-30) REVERT: A 348 LYS cc_start: 0.5224 (mtmm) cc_final: 0.4887 (tttp) REVERT: A 458 GLN cc_start: 0.7129 (mm110) cc_final: 0.6626 (tm-30) REVERT: A 481 ARG cc_start: 0.5293 (ptm160) cc_final: 0.4756 (ptp-170) REVERT: A 603 HIS cc_start: 0.5854 (m-70) cc_final: 0.5509 (m90) REVERT: A 687 PHE cc_start: 0.4626 (m-80) cc_final: 0.4319 (m-10) REVERT: A 780 ILE cc_start: 0.3429 (OUTLIER) cc_final: 0.3218 (pp) REVERT: A 835 LEU cc_start: 0.3384 (mt) cc_final: 0.2315 (mp) REVERT: A 1120 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.4610 (t80) REVERT: A 1175 MET cc_start: 0.7245 (ttp) cc_final: 0.6997 (ttp) REVERT: A 1294 MET cc_start: 0.4769 (mtt) cc_final: 0.4503 (ttm) REVERT: A 1439 MET cc_start: 0.2232 (mtm) cc_final: 0.1176 (tpt) REVERT: A 1620 GLN cc_start: 0.6891 (tp40) cc_final: 0.6300 (mp10) REVERT: A 1631 ARG cc_start: 0.6063 (ttm170) cc_final: 0.5592 (ttm110) REVERT: B 39 GLN cc_start: 0.5048 (mp10) cc_final: 0.4108 (mp10) REVERT: B 205 MET cc_start: 0.3815 (mpp) cc_final: 0.2975 (mtm) REVERT: B 244 THR cc_start: -0.1019 (OUTLIER) cc_final: -0.1532 (p) REVERT: B 268 GLU cc_start: 0.7827 (mp0) cc_final: 0.7367 (mp0) REVERT: B 315 LYS cc_start: 0.6670 (tttm) cc_final: 0.6327 (mmtt) REVERT: B 411 MET cc_start: 0.3998 (tpt) cc_final: 0.2426 (ttp) REVERT: B 502 MET cc_start: 0.3797 (ttt) cc_final: 0.3562 (ttt) REVERT: B 593 ILE cc_start: 0.2458 (OUTLIER) cc_final: 0.2117 (tt) REVERT: B 649 MET cc_start: 0.2071 (mtt) cc_final: 0.1519 (ptp) REVERT: B 1010 ASN cc_start: 0.4003 (m-40) cc_final: 0.3773 (m110) REVERT: C 74 GLU cc_start: 0.5138 (mp0) cc_final: 0.4589 (tp30) REVERT: C 224 THR cc_start: 0.3721 (m) cc_final: 0.3514 (m) REVERT: C 298 PHE cc_start: 0.3829 (m-10) cc_final: 0.3367 (m-10) REVERT: C 308 MET cc_start: 0.3009 (tpt) cc_final: 0.1536 (mtm) REVERT: D 35 GLU cc_start: 0.7392 (mp0) cc_final: 0.7168 (mp0) REVERT: E 94 LYS cc_start: 0.6230 (mttt) cc_final: 0.6008 (ptpp) REVERT: G 52 MET cc_start: 0.6690 (tmm) cc_final: 0.6444 (tmm) REVERT: G 238 THR cc_start: 0.3492 (OUTLIER) cc_final: 0.3209 (p) REVERT: G 241 ARG cc_start: 0.5669 (mtm-85) cc_final: 0.4076 (mpt180) REVERT: H 10 PHE cc_start: 0.4554 (m-10) cc_final: 0.3995 (m-10) REVERT: H 146 ARG cc_start: 0.5175 (mtt-85) cc_final: 0.4665 (ttm-80) REVERT: K 74 ASN cc_start: 0.5703 (t0) cc_final: 0.4693 (p0) REVERT: N 107 MET cc_start: 0.4988 (mmp) cc_final: 0.4202 (mmt) REVERT: O 182 MET cc_start: 0.0821 (ttt) cc_final: -0.0925 (tmm) REVERT: O 190 ILE cc_start: 0.4910 (mt) cc_final: 0.4449 (mt) REVERT: O 230 TRP cc_start: 0.4477 (m100) cc_final: 0.3827 (m100) REVERT: O 467 MET cc_start: 0.4447 (mmp) cc_final: 0.3810 (mmt) REVERT: O 581 THR cc_start: 0.5636 (p) cc_final: 0.5406 (t) REVERT: O 608 GLU cc_start: 0.3051 (tm-30) cc_final: 0.2022 (pm20) REVERT: S 16 LEU cc_start: 0.3854 (OUTLIER) cc_final: 0.3535 (mp) REVERT: S 21 GLN cc_start: 0.5278 (tt0) cc_final: 0.4921 (mp-120) REVERT: S 43 LEU cc_start: 0.2697 (OUTLIER) cc_final: 0.2454 (tt) REVERT: S 305 PHE cc_start: 0.5772 (m-10) cc_final: 0.5129 (t80) REVERT: S 344 ILE cc_start: 0.3669 (mm) cc_final: 0.3326 (pt) REVERT: S 360 TRP cc_start: 0.3335 (OUTLIER) cc_final: 0.2679 (t-100) REVERT: S 415 LEU cc_start: 0.2806 (tt) cc_final: 0.1011 (mt) REVERT: S 419 ARG cc_start: 0.6064 (ptt90) cc_final: 0.5439 (ptm160) REVERT: S 478 MET cc_start: 0.3355 (OUTLIER) cc_final: 0.3101 (ptm) REVERT: S 614 GLU cc_start: 0.5582 (mt-10) cc_final: 0.5344 (tm-30) REVERT: S 639 GLU cc_start: 0.2284 (mm-30) cc_final: 0.2071 (mm-30) REVERT: S 686 TYR cc_start: 0.0468 (m-80) cc_final: 0.0011 (m-80) REVERT: S 744 LEU cc_start: 0.4435 (OUTLIER) cc_final: 0.3848 (mp) REVERT: S 777 MET cc_start: 0.1820 (ppp) cc_final: 0.1231 (ttt) REVERT: R 173 MET cc_start: 0.4674 (tpt) cc_final: 0.4065 (tpt) REVERT: R 274 MET cc_start: 0.4087 (ptt) cc_final: 0.3059 (tpp) outliers start: 138 outliers final: 66 residues processed: 894 average time/residue: 0.5191 time to fit residues: 774.4320 Evaluate side-chains 656 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 579 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain G residue 16 PHE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 360 TRP Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 744 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 308 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 461 optimal weight: 7.9990 chunk 377 optimal weight: 0.8980 chunk 153 optimal weight: 0.0070 chunk 555 optimal weight: 7.9990 chunk 600 optimal weight: 0.8980 chunk 495 optimal weight: 5.9990 chunk 551 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 445 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 507 ASN M 89 GLN ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 489 ASN A 559 ASN A 560 GLN A 819 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN A1323 HIS A1503 HIS ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 673 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B 899 GLN B1041 ASN B1082 HIS B1115 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 GLN G 128 GLN H 11 GLN J 53 HIS K 64 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 HIS S 346 ASN S 720 GLN R 184 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3991 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 52007 Z= 0.224 Angle : 0.686 12.692 70659 Z= 0.357 Chirality : 0.044 0.316 7878 Planarity : 0.005 0.080 8735 Dihedral : 14.265 179.171 7612 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.93 % Allowed : 11.96 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.10), residues: 5986 helix: -2.43 (0.09), residues: 2066 sheet: -2.05 (0.19), residues: 690 loop : -2.26 (0.10), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 380 HIS 0.018 0.001 HIS O 472 PHE 0.028 0.002 PHE S 675 TYR 0.030 0.002 TYR A 97 ARG 0.009 0.001 ARG A1288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 699 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.4036 (ttp) cc_final: 0.1973 (mmp) REVERT: Q 179 CYS cc_start: 0.2891 (t) cc_final: 0.2205 (p) REVERT: Q 252 LEU cc_start: 0.3519 (tt) cc_final: 0.3144 (tp) REVERT: M 47 GLU cc_start: -0.1999 (OUTLIER) cc_final: -0.2592 (mt-10) REVERT: A 199 ASP cc_start: 0.6077 (m-30) cc_final: 0.5705 (m-30) REVERT: A 424 MET cc_start: 0.2083 (tmm) cc_final: 0.1644 (ppp) REVERT: A 458 GLN cc_start: 0.7115 (mm110) cc_final: 0.6712 (tm-30) REVERT: A 481 ARG cc_start: 0.4917 (ptm160) cc_final: 0.4160 (ptp-170) REVERT: A 673 HIS cc_start: 0.5276 (m170) cc_final: 0.4911 (m170) REVERT: A 797 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.6008 (tp) REVERT: A 1057 ILE cc_start: 0.6747 (mp) cc_final: 0.6495 (mt) REVERT: A 1116 GLN cc_start: 0.4156 (mm110) cc_final: 0.3598 (mm-40) REVERT: A 1120 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5198 (t80) REVERT: A 1439 MET cc_start: 0.2245 (mtm) cc_final: 0.1730 (tpp) REVERT: A 1441 LYS cc_start: 0.5823 (tptp) cc_final: 0.5423 (mmmt) REVERT: A 1501 ILE cc_start: 0.3776 (tp) cc_final: 0.3366 (mm) REVERT: A 1620 GLN cc_start: 0.6865 (tp40) cc_final: 0.6347 (mp10) REVERT: A 1631 ARG cc_start: 0.6177 (ttm170) cc_final: 0.5698 (ttm110) REVERT: B 39 GLN cc_start: 0.5167 (mp10) cc_final: 0.4560 (mp10) REVERT: B 143 TRP cc_start: 0.5562 (OUTLIER) cc_final: 0.5107 (m100) REVERT: B 268 GLU cc_start: 0.7744 (mp0) cc_final: 0.7327 (mp0) REVERT: B 315 LYS cc_start: 0.6474 (tttm) cc_final: 0.6203 (mmtt) REVERT: B 316 ARG cc_start: 0.5068 (tpt90) cc_final: 0.4374 (ptp-170) REVERT: B 411 MET cc_start: 0.3548 (tpt) cc_final: 0.2561 (ttp) REVERT: B 446 MET cc_start: 0.3913 (ttt) cc_final: 0.3561 (ttt) REVERT: B 451 MET cc_start: 0.5688 (tpt) cc_final: 0.5159 (ptm) REVERT: B 502 MET cc_start: 0.4404 (ttt) cc_final: 0.3982 (ttm) REVERT: B 649 MET cc_start: 0.2800 (mtt) cc_final: 0.2172 (ptp) REVERT: B 702 ASN cc_start: 0.5511 (t0) cc_final: 0.4853 (t0) REVERT: B 721 MET cc_start: 0.5283 (tpp) cc_final: 0.4843 (tpp) REVERT: B 963 PHE cc_start: 0.3057 (m-80) cc_final: 0.2401 (m-80) REVERT: B 1097 ASP cc_start: 0.6368 (p0) cc_final: 0.5642 (p0) REVERT: C 72 ILE cc_start: 0.7022 (mt) cc_final: 0.6792 (mt) REVERT: C 74 GLU cc_start: 0.5026 (mp0) cc_final: 0.4709 (tp30) REVERT: C 249 LYS cc_start: 0.5200 (OUTLIER) cc_final: 0.3928 (tttp) REVERT: C 308 MET cc_start: 0.3598 (tpt) cc_final: 0.2601 (mtt) REVERT: C 310 PRO cc_start: 0.3798 (Cg_endo) cc_final: 0.3496 (Cg_exo) REVERT: D 37 LEU cc_start: 0.8552 (tt) cc_final: 0.8114 (mt) REVERT: E 93 MET cc_start: 0.3987 (OUTLIER) cc_final: 0.3018 (tmm) REVERT: E 99 HIS cc_start: 0.6111 (t70) cc_final: 0.5889 (t70) REVERT: E 121 MET cc_start: 0.4763 (tpt) cc_final: 0.3644 (mmt) REVERT: E 215 MET cc_start: 0.3018 (ptp) cc_final: 0.1520 (mtt) REVERT: F 109 VAL cc_start: 0.3829 (p) cc_final: 0.3609 (p) REVERT: G 52 MET cc_start: 0.6408 (tmm) cc_final: 0.6045 (tmm) REVERT: G 241 ARG cc_start: 0.5528 (mtm-85) cc_final: 0.4017 (mpt180) REVERT: K 74 ASN cc_start: 0.6014 (t0) cc_final: 0.5295 (p0) REVERT: K 88 PHE cc_start: 0.3299 (t80) cc_final: 0.0896 (t80) REVERT: K 101 LEU cc_start: 0.6142 (tt) cc_final: 0.5826 (tp) REVERT: K 142 MET cc_start: 0.5080 (mpp) cc_final: 0.4733 (mpp) REVERT: O 182 MET cc_start: 0.0479 (ttt) cc_final: -0.1203 (tmm) REVERT: O 396 MET cc_start: 0.5856 (mtp) cc_final: 0.5554 (mtp) REVERT: O 467 MET cc_start: 0.4686 (mmp) cc_final: 0.4035 (mmt) REVERT: O 472 HIS cc_start: 0.3499 (OUTLIER) cc_final: 0.3150 (m90) REVERT: O 525 MET cc_start: 0.3113 (ttm) cc_final: 0.2224 (mtt) REVERT: O 581 THR cc_start: 0.5745 (p) cc_final: 0.5515 (t) REVERT: O 608 GLU cc_start: 0.3124 (tm-30) cc_final: 0.2057 (pm20) REVERT: S 43 LEU cc_start: 0.2481 (OUTLIER) cc_final: 0.2130 (tt) REVERT: S 247 ILE cc_start: 0.3768 (OUTLIER) cc_final: 0.3556 (mp) REVERT: S 305 PHE cc_start: 0.5744 (m-10) cc_final: 0.5203 (t80) REVERT: S 344 ILE cc_start: 0.3825 (mm) cc_final: 0.3546 (pt) REVERT: S 415 LEU cc_start: 0.3026 (tt) cc_final: 0.1256 (mt) REVERT: S 478 MET cc_start: 0.3457 (OUTLIER) cc_final: 0.3218 (ptm) REVERT: S 614 GLU cc_start: 0.5600 (mt-10) cc_final: 0.5218 (tm-30) REVERT: S 706 GLU cc_start: 0.5440 (tp30) cc_final: 0.4072 (mt-10) REVERT: S 744 LEU cc_start: 0.4189 (OUTLIER) cc_final: 0.3336 (mp) REVERT: R 168 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4350 (mp) REVERT: R 253 ILE cc_start: 0.2459 (OUTLIER) cc_final: 0.2233 (pp) outliers start: 160 outliers final: 82 residues processed: 814 average time/residue: 0.5076 time to fit residues: 701.0162 Evaluate side-chains 641 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 546 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1082 HIS Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 744 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 253 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 549 optimal weight: 5.9990 chunk 417 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 chunk 373 optimal weight: 6.9990 chunk 557 optimal weight: 0.6980 chunk 590 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 528 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 434 HIS ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 560 GLN A 590 ASN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN B1114 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS C 234 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN E 8 ASN E 146 HIS G 23 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 GLN S 58 HIS S 232 ASN S 323 ASN S 368 HIS R 184 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 52007 Z= 0.312 Angle : 0.811 17.927 70659 Z= 0.421 Chirality : 0.049 0.402 7878 Planarity : 0.007 0.133 8735 Dihedral : 14.358 178.865 7610 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.45 % Favored : 92.53 % Rotamer: Outliers : 3.80 % Allowed : 12.77 % Favored : 83.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.10), residues: 5986 helix: -2.08 (0.10), residues: 2041 sheet: -2.05 (0.19), residues: 687 loop : -2.16 (0.10), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP Q 316 HIS 0.088 0.002 HIS B1082 PHE 0.058 0.003 PHE R 366 TYR 0.043 0.003 TYR A 995 ARG 0.016 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 799 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.4132 (ttp) cc_final: 0.2149 (mmp) REVERT: Q 381 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5938 (tpp) REVERT: Q 412 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7359 (tptm) REVERT: Q 419 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4495 (tp) REVERT: Q 488 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5312 (mt) REVERT: M 47 GLU cc_start: -0.1741 (OUTLIER) cc_final: -0.2419 (mt-10) REVERT: A 199 ASP cc_start: 0.6115 (m-30) cc_final: 0.5893 (m-30) REVERT: A 242 LYS cc_start: 0.0878 (OUTLIER) cc_final: 0.0641 (tttp) REVERT: A 357 MET cc_start: 0.2870 (tpt) cc_final: 0.1590 (ptm) REVERT: A 388 LYS cc_start: 0.7025 (ttmp) cc_final: 0.6479 (mptt) REVERT: A 424 MET cc_start: 0.3080 (tmm) cc_final: 0.2519 (ppp) REVERT: A 458 GLN cc_start: 0.7148 (mm110) cc_final: 0.6878 (tm-30) REVERT: A 462 LYS cc_start: 0.5568 (mttt) cc_final: 0.5352 (ttmt) REVERT: A 481 ARG cc_start: 0.5097 (ptm160) cc_final: 0.4099 (ptp-170) REVERT: A 529 LYS cc_start: 0.4174 (OUTLIER) cc_final: 0.3371 (tttp) REVERT: A 589 MET cc_start: 0.5106 (ttt) cc_final: 0.3927 (mmt) REVERT: A 759 TYR cc_start: 0.6007 (m-80) cc_final: 0.5728 (m-80) REVERT: A 930 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.4525 (tp) REVERT: A 946 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7127 (pp) REVERT: A 1000 MET cc_start: 0.5498 (tpp) cc_final: 0.5257 (ttt) REVERT: A 1053 ASP cc_start: 0.5572 (t0) cc_final: 0.5269 (t0) REVERT: A 1057 ILE cc_start: 0.7649 (mp) cc_final: 0.7294 (mm) REVERT: A 1120 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.5477 (t80) REVERT: A 1143 LYS cc_start: 0.6743 (mttt) cc_final: 0.5885 (tttt) REVERT: A 1227 MET cc_start: 0.2163 (mmt) cc_final: 0.1812 (mmm) REVERT: A 1238 MET cc_start: 0.4848 (tpp) cc_final: 0.4082 (tpp) REVERT: A 1269 LYS cc_start: 0.4878 (mtmt) cc_final: 0.4569 (mptt) REVERT: A 1301 GLU cc_start: 0.3876 (OUTLIER) cc_final: 0.3529 (tt0) REVERT: A 1329 ILE cc_start: 0.6806 (mt) cc_final: 0.6513 (pt) REVERT: A 1441 LYS cc_start: 0.5350 (tptp) cc_final: 0.4622 (mmtt) REVERT: A 1485 MET cc_start: 0.4556 (mtt) cc_final: 0.4292 (mtp) REVERT: A 1490 GLU cc_start: 0.4622 (mt-10) cc_final: 0.4073 (mt-10) REVERT: A 1501 ILE cc_start: 0.4380 (tp) cc_final: 0.3806 (mm) REVERT: A 1620 GLN cc_start: 0.7368 (tp40) cc_final: 0.6696 (mp10) REVERT: A 1631 ARG cc_start: 0.6878 (ttm170) cc_final: 0.6256 (ttm110) REVERT: B 39 GLN cc_start: 0.5049 (mp10) cc_final: 0.4267 (mp10) REVERT: B 168 ASN cc_start: 0.6096 (m110) cc_final: 0.5674 (p0) REVERT: B 200 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: B 207 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5605 (mm) REVERT: B 316 ARG cc_start: 0.5098 (tpt90) cc_final: 0.4339 (ptp-170) REVERT: B 388 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6453 (mm-30) REVERT: B 649 MET cc_start: 0.5164 (mtt) cc_final: 0.4507 (mmt) REVERT: B 672 MET cc_start: 0.2987 (mmm) cc_final: 0.2007 (ptt) REVERT: B 702 ASN cc_start: 0.6712 (t0) cc_final: 0.6232 (t0) REVERT: B 882 ILE cc_start: 0.5918 (mp) cc_final: 0.5222 (mm) REVERT: B 904 LYS cc_start: 0.5959 (ttmm) cc_final: 0.5366 (ttpt) REVERT: B 936 MET cc_start: 0.7824 (mmt) cc_final: 0.7223 (mmt) REVERT: B 1053 ASN cc_start: 0.6062 (t0) cc_final: 0.5803 (t0) REVERT: C 72 ILE cc_start: 0.8163 (mt) cc_final: 0.7916 (mt) REVERT: C 136 LEU cc_start: 0.5494 (tp) cc_final: 0.5190 (tp) REVERT: C 192 LEU cc_start: 0.7804 (tt) cc_final: 0.7579 (tp) REVERT: C 311 GLU cc_start: 0.5300 (pm20) cc_final: 0.4972 (mp0) REVERT: D 37 LEU cc_start: 0.8609 (tt) cc_final: 0.8334 (mt) REVERT: E 121 MET cc_start: 0.5226 (tpt) cc_final: 0.3973 (mmt) REVERT: E 215 MET cc_start: 0.5154 (ptp) cc_final: 0.3508 (mtt) REVERT: F 118 LEU cc_start: 0.4971 (tp) cc_final: 0.4603 (tt) REVERT: G 52 MET cc_start: 0.6475 (tmm) cc_final: 0.6079 (tmm) REVERT: G 241 ARG cc_start: 0.4932 (mtm-85) cc_final: 0.3510 (mpt180) REVERT: J 4 PRO cc_start: 0.7256 (Cg_exo) cc_final: 0.6946 (Cg_endo) REVERT: J 44 TYR cc_start: 0.6737 (p90) cc_final: 0.6530 (p90) REVERT: K 74 ASN cc_start: 0.6745 (t0) cc_final: 0.5883 (p0) REVERT: K 142 MET cc_start: 0.4644 (mpp) cc_final: 0.4212 (mpp) REVERT: N 58 PHE cc_start: 0.5892 (m-80) cc_final: 0.5610 (m-80) REVERT: N 107 MET cc_start: 0.5381 (mmp) cc_final: 0.4677 (mmt) REVERT: N 169 GLU cc_start: 0.5800 (pt0) cc_final: 0.3887 (pt0) REVERT: O 182 MET cc_start: 0.0306 (ttt) cc_final: -0.1247 (tmm) REVERT: O 396 MET cc_start: 0.5736 (mtp) cc_final: 0.5426 (mtp) REVERT: O 467 MET cc_start: 0.4826 (mmp) cc_final: 0.4260 (mmt) REVERT: O 472 HIS cc_start: 0.4339 (t-90) cc_final: 0.3873 (m170) REVERT: O 521 ASN cc_start: 0.3819 (t0) cc_final: 0.3595 (t0) REVERT: O 608 GLU cc_start: 0.3169 (tm-30) cc_final: 0.2241 (pm20) REVERT: S 305 PHE cc_start: 0.5603 (m-10) cc_final: 0.5155 (t80) REVERT: S 344 ILE cc_start: 0.3930 (mm) cc_final: 0.3653 (pt) REVERT: S 351 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.4543 (mp) REVERT: S 405 TYR cc_start: 0.6706 (t80) cc_final: 0.5853 (t80) REVERT: S 476 ILE cc_start: 0.4240 (tp) cc_final: 0.3922 (mm) REVERT: S 614 GLU cc_start: 0.6074 (mt-10) cc_final: 0.5294 (pp20) REVERT: S 706 GLU cc_start: 0.5576 (tp30) cc_final: 0.4220 (mt-10) REVERT: R 274 MET cc_start: 0.4004 (tpp) cc_final: 0.3414 (tpp) REVERT: R 401 ILE cc_start: 0.4265 (OUTLIER) cc_final: 0.3994 (tt) outliers start: 208 outliers final: 96 residues processed: 939 average time/residue: 0.5128 time to fit residues: 811.7541 Evaluate side-chains 714 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 604 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 381 MET Chi-restraints excluded: chain Q residue 419 LEU Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain R residue 401 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 491 optimal weight: 2.9990 chunk 335 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 439 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 503 optimal weight: 8.9990 chunk 408 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 530 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 82 ASN M 89 GLN A 26 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 560 GLN A 785 GLN A 819 ASN A 923 ASN A 949 GLN A1113 HIS A1525 ASN B 50 ASN B 173 ASN B 282 HIS B 399 HIS ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 745 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 HIS ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 23 GLN G 26 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 368 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5320 moved from start: 0.9154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 52007 Z= 0.320 Angle : 0.774 17.583 70659 Z= 0.400 Chirality : 0.048 0.347 7878 Planarity : 0.006 0.092 8735 Dihedral : 14.301 179.082 7610 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.03 % Favored : 92.95 % Rotamer: Outliers : 3.49 % Allowed : 15.62 % Favored : 80.89 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.10), residues: 5986 helix: -1.84 (0.10), residues: 2080 sheet: -2.07 (0.19), residues: 685 loop : -2.11 (0.10), residues: 3221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP S 360 HIS 0.031 0.002 HIS B1082 PHE 0.035 0.003 PHE B 313 TYR 0.027 0.002 TYR J 21 ARG 0.019 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 767 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3707 (ttp) cc_final: 0.1935 (mmp) REVERT: Q 317 MET cc_start: 0.4882 (mmt) cc_final: 0.4386 (tpt) REVERT: Q 381 MET cc_start: 0.5480 (tpt) cc_final: 0.5143 (tpt) REVERT: Q 412 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7420 (tptm) REVERT: Q 488 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5271 (mt) REVERT: M 47 GLU cc_start: -0.1545 (OUTLIER) cc_final: -0.2126 (mt-10) REVERT: M 50 GLU cc_start: 0.5931 (mt-10) cc_final: 0.5153 (pt0) REVERT: A 199 ASP cc_start: 0.6284 (m-30) cc_final: 0.6056 (m-30) REVERT: A 225 LYS cc_start: 0.7256 (ptpt) cc_final: 0.6947 (ptpp) REVERT: A 238 MET cc_start: -0.1442 (mmp) cc_final: -0.1713 (mmp) REVERT: A 242 LYS cc_start: 0.0865 (OUTLIER) cc_final: 0.0537 (tttp) REVERT: A 325 ASP cc_start: 0.6010 (t0) cc_final: 0.5746 (p0) REVERT: A 357 MET cc_start: 0.3160 (tpt) cc_final: 0.1964 (ptm) REVERT: A 388 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6519 (mmtt) REVERT: A 424 MET cc_start: 0.2602 (tmm) cc_final: 0.1895 (ppp) REVERT: A 549 MET cc_start: 0.5433 (mmt) cc_final: 0.5093 (mpp) REVERT: A 560 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6321 (tp-100) REVERT: A 597 LYS cc_start: 0.5971 (ttpt) cc_final: 0.5477 (mptt) REVERT: A 678 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7836 (t) REVERT: A 712 ILE cc_start: 0.6546 (mt) cc_final: 0.6268 (mt) REVERT: A 925 MET cc_start: 0.5253 (mmp) cc_final: 0.4914 (mmp) REVERT: A 930 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.5776 (tp) REVERT: A 1060 GLU cc_start: 0.6029 (pt0) cc_final: 0.5317 (tt0) REVERT: A 1120 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.5312 (t80) REVERT: A 1227 MET cc_start: 0.3432 (mmt) cc_final: 0.3035 (mmm) REVERT: A 1269 LYS cc_start: 0.6072 (mtmt) cc_final: 0.5776 (mptt) REVERT: A 1441 LYS cc_start: 0.5227 (tptp) cc_final: 0.4729 (mmtt) REVERT: A 1485 MET cc_start: 0.4626 (mtt) cc_final: 0.4174 (mtp) REVERT: A 1592 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7217 (tp40) REVERT: A 1616 GLU cc_start: 0.5008 (pt0) cc_final: 0.4378 (pp20) REVERT: A 1620 GLN cc_start: 0.7482 (tp40) cc_final: 0.6748 (mp10) REVERT: A 1631 ARG cc_start: 0.6923 (ttm170) cc_final: 0.6557 (ttm110) REVERT: B 74 PHE cc_start: 0.3842 (m-80) cc_final: 0.3623 (m-80) REVERT: B 153 PHE cc_start: 0.7965 (m-10) cc_final: 0.7532 (m-80) REVERT: B 164 MET cc_start: 0.6484 (ttm) cc_final: 0.6231 (ttm) REVERT: B 388 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6549 (tp30) REVERT: B 421 LEU cc_start: 0.7275 (mm) cc_final: 0.6841 (mm) REVERT: B 672 MET cc_start: 0.4693 (mmm) cc_final: 0.3354 (ptt) REVERT: B 702 ASN cc_start: 0.7119 (t0) cc_final: 0.6869 (t0) REVERT: B 723 LYS cc_start: 0.6926 (mttt) cc_final: 0.6593 (mtpt) REVERT: B 782 ASP cc_start: 0.8292 (p0) cc_final: 0.8052 (p0) REVERT: B 882 ILE cc_start: 0.5810 (mp) cc_final: 0.4803 (mm) REVERT: B 886 ASN cc_start: 0.7586 (m-40) cc_final: 0.6156 (p0) REVERT: B 1053 ASN cc_start: 0.6568 (t0) cc_final: 0.6348 (t0) REVERT: B 1057 MET cc_start: 0.6085 (ptm) cc_final: 0.5796 (ptm) REVERT: B 1097 ASP cc_start: 0.6437 (p0) cc_final: 0.5702 (p0) REVERT: B 1192 MET cc_start: 0.4454 (pmm) cc_final: 0.4048 (pmm) REVERT: C 100 ARG cc_start: 0.7409 (mtt90) cc_final: 0.6073 (ttm-80) REVERT: C 192 LEU cc_start: 0.8488 (tt) cc_final: 0.8135 (tp) REVERT: D 2 MET cc_start: 0.1913 (tpt) cc_final: -0.0236 (mmt) REVERT: E 22 MET cc_start: 0.5657 (ttp) cc_final: 0.5117 (ttt) REVERT: E 79 TRP cc_start: 0.6661 (t-100) cc_final: 0.6257 (t-100) REVERT: E 93 MET cc_start: 0.3887 (OUTLIER) cc_final: 0.2793 (tmm) REVERT: E 121 MET cc_start: 0.5390 (tpt) cc_final: 0.4254 (mmt) REVERT: E 164 LEU cc_start: 0.7063 (tp) cc_final: 0.6708 (tp) REVERT: E 166 LYS cc_start: 0.8142 (tttt) cc_final: 0.7814 (mmtt) REVERT: E 215 MET cc_start: 0.4959 (ptp) cc_final: 0.4338 (mtt) REVERT: F 128 LYS cc_start: 0.5750 (mmtt) cc_final: 0.4978 (tppt) REVERT: F 137 TYR cc_start: 0.5929 (m-80) cc_final: 0.5105 (m-80) REVERT: F 138 LEU cc_start: 0.6499 (mp) cc_final: 0.6254 (mp) REVERT: G 52 MET cc_start: 0.6431 (tmm) cc_final: 0.5983 (tmm) REVERT: G 119 HIS cc_start: 0.4276 (t-90) cc_final: 0.3901 (t-90) REVERT: G 241 ARG cc_start: 0.4343 (mtm-85) cc_final: 0.3202 (mpt180) REVERT: H 52 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6731 (mm-40) REVERT: H 64 ASN cc_start: 0.6888 (t0) cc_final: 0.6525 (t0) REVERT: I 53 ASP cc_start: 0.7205 (p0) cc_final: 0.6570 (t0) REVERT: J 44 TYR cc_start: 0.7435 (p90) cc_final: 0.7228 (p90) REVERT: K 45 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6215 (mt-10) REVERT: K 103 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6389 (tt) REVERT: K 110 GLU cc_start: 0.5864 (pt0) cc_final: 0.5053 (tp30) REVERT: N 58 PHE cc_start: 0.6367 (m-80) cc_final: 0.5872 (m-80) REVERT: N 82 ILE cc_start: 0.3875 (OUTLIER) cc_final: 0.3338 (tt) REVERT: O 70 GLN cc_start: 0.3921 (tp40) cc_final: 0.3502 (tt0) REVERT: O 156 MET cc_start: -0.0177 (OUTLIER) cc_final: -0.0480 (mmm) REVERT: O 187 MET cc_start: 0.4568 (mmp) cc_final: 0.3531 (mtt) REVERT: O 243 GLU cc_start: 0.5551 (mt-10) cc_final: 0.4343 (tp30) REVERT: O 396 MET cc_start: 0.6288 (mtp) cc_final: 0.5773 (mtp) REVERT: O 467 MET cc_start: 0.5886 (mmp) cc_final: 0.5339 (mmt) REVERT: O 525 MET cc_start: 0.3237 (ttm) cc_final: 0.2915 (ttm) REVERT: O 608 GLU cc_start: 0.3114 (tm-30) cc_final: 0.2265 (pm20) REVERT: S 300 LEU cc_start: 0.4675 (pt) cc_final: 0.4421 (mp) REVERT: S 305 PHE cc_start: 0.5572 (m-10) cc_final: 0.5206 (t80) REVERT: S 345 ASP cc_start: 0.5588 (t0) cc_final: 0.5196 (m-30) REVERT: S 471 MET cc_start: 0.3498 (ttm) cc_final: 0.3267 (ttm) REVERT: S 614 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5417 (pp20) REVERT: S 744 LEU cc_start: 0.3825 (tt) cc_final: 0.3110 (mp) REVERT: S 777 MET cc_start: 0.2547 (ppp) cc_final: 0.2096 (tmm) REVERT: R 175 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.5838 (mt) REVERT: R 274 MET cc_start: 0.5579 (tpp) cc_final: 0.4902 (tpp) REVERT: R 401 ILE cc_start: 0.4820 (OUTLIER) cc_final: 0.4460 (tt) outliers start: 191 outliers final: 101 residues processed: 895 average time/residue: 0.4991 time to fit residues: 757.1945 Evaluate side-chains 715 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 600 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 416 LYS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 465 VAL Chi-restraints excluded: chain S residue 555 THR Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 401 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 198 optimal weight: 0.6980 chunk 531 optimal weight: 0.0370 chunk 116 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 591 optimal weight: 0.6980 chunk 490 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 GLN A1503 HIS B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 724 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 HIS ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 297 HIS C 301 ASN D 10 ASN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS K 74 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 438 GLN O 472 HIS S 613 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5332 moved from start: 0.9605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 52007 Z= 0.197 Angle : 0.656 15.078 70659 Z= 0.336 Chirality : 0.044 0.309 7878 Planarity : 0.005 0.082 8735 Dihedral : 14.119 179.002 7610 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.62 % Allowed : 17.63 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 5986 helix: -1.53 (0.10), residues: 2077 sheet: -1.90 (0.20), residues: 641 loop : -1.98 (0.10), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 611 HIS 0.007 0.001 HIS A1503 PHE 0.040 0.002 PHE B 798 TYR 0.025 0.001 TYR A1573 ARG 0.009 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 673 time to evaluate : 4.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3705 (ttp) cc_final: 0.1977 (mmp) REVERT: Q 190 MET cc_start: 0.7603 (tpp) cc_final: 0.7290 (tpp) REVERT: Q 381 MET cc_start: 0.5517 (tpt) cc_final: 0.5215 (tpt) REVERT: Q 412 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7334 (tptp) REVERT: Q 488 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5227 (mt) REVERT: M 47 GLU cc_start: -0.1526 (OUTLIER) cc_final: -0.2092 (mt-10) REVERT: M 50 GLU cc_start: 0.5871 (mt-10) cc_final: 0.5148 (pt0) REVERT: A 97 TYR cc_start: 0.5970 (m-80) cc_final: 0.5653 (m-80) REVERT: A 124 LEU cc_start: 0.6958 (mt) cc_final: 0.6703 (mt) REVERT: A 242 LYS cc_start: 0.0797 (OUTLIER) cc_final: 0.0462 (tttp) REVERT: A 325 ASP cc_start: 0.5996 (t0) cc_final: 0.5634 (p0) REVERT: A 357 MET cc_start: 0.3152 (tpt) cc_final: 0.1870 (ptm) REVERT: A 388 LYS cc_start: 0.6916 (ttmp) cc_final: 0.6418 (mptt) REVERT: A 424 MET cc_start: 0.2633 (tmm) cc_final: 0.2097 (ppp) REVERT: A 549 MET cc_start: 0.5360 (mmt) cc_final: 0.5026 (mpp) REVERT: A 560 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.6067 (tp-100) REVERT: A 600 MET cc_start: 0.5819 (tmm) cc_final: 0.5230 (tmm) REVERT: A 686 PHE cc_start: 0.8105 (m-80) cc_final: 0.7852 (m-80) REVERT: A 712 ILE cc_start: 0.6638 (mt) cc_final: 0.6362 (mt) REVERT: A 821 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5985 (pt) REVERT: A 925 MET cc_start: 0.5536 (mmp) cc_final: 0.5145 (mmp) REVERT: A 928 MET cc_start: 0.7714 (mtt) cc_final: 0.7492 (mtp) REVERT: A 1060 GLU cc_start: 0.5961 (pt0) cc_final: 0.5419 (tt0) REVERT: A 1120 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.5625 (t80) REVERT: A 1269 LYS cc_start: 0.5751 (mtmt) cc_final: 0.5474 (mptt) REVERT: A 1579 PHE cc_start: 0.6930 (m-80) cc_final: 0.6730 (m-80) REVERT: A 1592 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7267 (tp40) REVERT: A 1616 GLU cc_start: 0.5452 (pt0) cc_final: 0.4819 (pp20) REVERT: A 1620 GLN cc_start: 0.7453 (tp40) cc_final: 0.6722 (mp10) REVERT: A 1631 ARG cc_start: 0.6689 (ttm170) cc_final: 0.5990 (mtp-110) REVERT: B 164 MET cc_start: 0.6568 (ttm) cc_final: 0.6331 (ttm) REVERT: B 203 ILE cc_start: 0.7414 (mm) cc_final: 0.7166 (mm) REVERT: B 205 MET cc_start: 0.6675 (mpp) cc_final: 0.6190 (ptp) REVERT: B 372 ARG cc_start: 0.7592 (mtm110) cc_final: 0.6767 (mtm110) REVERT: B 388 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6559 (tp30) REVERT: B 408 LEU cc_start: 0.7924 (pp) cc_final: 0.7512 (tp) REVERT: B 421 LEU cc_start: 0.7251 (mm) cc_final: 0.6959 (mm) REVERT: B 545 PHE cc_start: 0.6561 (m-10) cc_final: 0.6345 (m-80) REVERT: B 672 MET cc_start: 0.4635 (mmm) cc_final: 0.3389 (ptt) REVERT: B 702 ASN cc_start: 0.7407 (t0) cc_final: 0.7132 (t0) REVERT: B 723 LYS cc_start: 0.7035 (mttt) cc_final: 0.6795 (mtpt) REVERT: B 769 PHE cc_start: 0.7415 (p90) cc_final: 0.7135 (p90) REVERT: B 882 ILE cc_start: 0.6133 (mp) cc_final: 0.5710 (mp) REVERT: B 1053 ASN cc_start: 0.6480 (t0) cc_final: 0.6245 (t0) REVERT: B 1082 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5971 (m170) REVERT: B 1097 ASP cc_start: 0.6648 (p0) cc_final: 0.5997 (p0) REVERT: B 1192 MET cc_start: 0.4445 (pmm) cc_final: 0.4024 (pmm) REVERT: C 100 ARG cc_start: 0.7443 (mtt90) cc_final: 0.6038 (ttm-80) REVERT: C 192 LEU cc_start: 0.8363 (tt) cc_final: 0.7976 (tp) REVERT: C 293 ARG cc_start: 0.5245 (mmt90) cc_final: 0.4959 (mmt90) REVERT: D 2 MET cc_start: 0.1862 (tpt) cc_final: -0.0467 (mmt) REVERT: E 22 MET cc_start: 0.6000 (ttp) cc_final: 0.5569 (ttt) REVERT: E 93 MET cc_start: 0.3988 (OUTLIER) cc_final: 0.2957 (tmm) REVERT: E 121 MET cc_start: 0.5375 (tpt) cc_final: 0.4185 (mmt) REVERT: E 164 LEU cc_start: 0.6719 (tp) cc_final: 0.6346 (tp) REVERT: E 166 LYS cc_start: 0.8091 (tttt) cc_final: 0.7690 (mmtt) REVERT: E 215 MET cc_start: 0.4794 (ptp) cc_final: 0.4429 (mtt) REVERT: F 60 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6457 (mm110) REVERT: F 128 LYS cc_start: 0.5754 (mmtt) cc_final: 0.5069 (tppt) REVERT: F 137 TYR cc_start: 0.5920 (m-80) cc_final: 0.5198 (m-80) REVERT: F 138 LEU cc_start: 0.6161 (mp) cc_final: 0.5874 (mp) REVERT: F 149 GLU cc_start: 0.7422 (tp30) cc_final: 0.7193 (tp30) REVERT: G 52 MET cc_start: 0.6327 (tmm) cc_final: 0.5783 (tmm) REVERT: G 119 HIS cc_start: 0.4125 (t-90) cc_final: 0.3778 (t-90) REVERT: G 241 ARG cc_start: 0.4665 (mtm-85) cc_final: 0.3518 (mpt180) REVERT: H 64 ASN cc_start: 0.7031 (t0) cc_final: 0.6564 (t0) REVERT: H 130 ARG cc_start: 0.4774 (ptp-170) cc_final: 0.3898 (ptp-170) REVERT: I 53 ASP cc_start: 0.7293 (p0) cc_final: 0.6607 (t0) REVERT: K 45 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6134 (mt-10) REVERT: K 110 GLU cc_start: 0.5773 (pt0) cc_final: 0.4946 (tp30) REVERT: N 58 PHE cc_start: 0.6219 (m-80) cc_final: 0.5940 (m-80) REVERT: N 107 MET cc_start: 0.5012 (mmp) cc_final: 0.4233 (mmt) REVERT: O 70 GLN cc_start: 0.3907 (tp40) cc_final: 0.3523 (tt0) REVERT: O 128 LEU cc_start: 0.3316 (mt) cc_final: 0.2628 (pt) REVERT: O 187 MET cc_start: 0.4224 (mmp) cc_final: 0.3018 (mtt) REVERT: O 243 GLU cc_start: 0.5602 (mt-10) cc_final: 0.4479 (tp30) REVERT: O 396 MET cc_start: 0.6173 (mtp) cc_final: 0.5718 (mtp) REVERT: O 467 MET cc_start: 0.5806 (mmp) cc_final: 0.5319 (mmt) REVERT: O 525 MET cc_start: 0.3229 (ttm) cc_final: 0.2893 (ttm) REVERT: O 608 GLU cc_start: 0.3116 (tm-30) cc_final: 0.2277 (pm20) REVERT: S 247 ILE cc_start: 0.4442 (OUTLIER) cc_final: 0.4143 (mp) REVERT: S 305 PHE cc_start: 0.5394 (m-10) cc_final: 0.5114 (t80) REVERT: S 345 ASP cc_start: 0.4980 (t0) cc_final: 0.4650 (t70) REVERT: S 369 PHE cc_start: 0.6594 (t80) cc_final: 0.6301 (t80) REVERT: S 476 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5180 (tp) REVERT: S 614 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5412 (pp20) REVERT: S 744 LEU cc_start: 0.3744 (tt) cc_final: 0.2924 (mp) REVERT: S 777 MET cc_start: 0.2746 (ppp) cc_final: 0.2274 (tmm) REVERT: R 27 ILE cc_start: 0.7519 (tt) cc_final: 0.7308 (tp) REVERT: R 175 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5701 (mt) REVERT: R 274 MET cc_start: 0.5218 (tpp) cc_final: 0.4562 (tpp) outliers start: 143 outliers final: 80 residues processed: 778 average time/residue: 0.5004 time to fit residues: 659.6485 Evaluate side-chains 670 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 579 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1082 HIS Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 476 ILE Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 569 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 336 optimal weight: 0.6980 chunk 431 optimal weight: 0.9990 chunk 334 optimal weight: 6.9990 chunk 497 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 588 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 209 ASN M 16 GLN M 82 ASN A 263 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 636 HIS A 753 ASN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 282 HIS B 462 GLN B 543 ASN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B 715 ASN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS G 170 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN N 85 HIS ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN S 37 GLN S 232 ASN S 267 ASN S 348 HIS S 368 HIS S 401 ASN R 184 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 1.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 52007 Z= 0.438 Angle : 0.940 15.527 70659 Z= 0.486 Chirality : 0.053 0.430 7878 Planarity : 0.007 0.094 8735 Dihedral : 14.677 178.265 7610 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.36 % Favored : 89.59 % Rotamer: Outliers : 3.64 % Allowed : 18.22 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.10), residues: 5986 helix: -1.96 (0.10), residues: 2032 sheet: -2.32 (0.19), residues: 701 loop : -2.31 (0.10), residues: 3253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP R 314 HIS 0.063 0.003 HIS B1082 PHE 0.044 0.004 PHE S 385 TYR 0.056 0.003 TYR A1290 ARG 0.016 0.001 ARG A1288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 714 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 19 LEU cc_start: 0.0381 (OUTLIER) cc_final: 0.0090 (mp) REVERT: Q 35 MET cc_start: 0.3660 (ttp) cc_final: 0.1798 (mmp) REVERT: Q 118 TRP cc_start: 0.6196 (t60) cc_final: 0.5501 (t60) REVERT: Q 153 LYS cc_start: 0.5594 (mtpt) cc_final: 0.5339 (mptt) REVERT: Q 183 LYS cc_start: 0.5281 (ttpp) cc_final: 0.4573 (mttt) REVERT: Q 360 LYS cc_start: 0.5674 (ptpt) cc_final: 0.4232 (mmtm) REVERT: Q 488 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5266 (mt) REVERT: M 47 GLU cc_start: -0.2144 (OUTLIER) cc_final: -0.2655 (mt-10) REVERT: M 50 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6233 (pt0) REVERT: M 80 LEU cc_start: 0.5337 (tp) cc_final: 0.4716 (tp) REVERT: A 43 HIS cc_start: 0.3999 (t-90) cc_final: 0.3408 (t-90) REVERT: A 225 LYS cc_start: 0.6863 (ptpt) cc_final: 0.6644 (ptpp) REVERT: A 242 LYS cc_start: 0.0738 (OUTLIER) cc_final: 0.0139 (tttp) REVERT: A 351 LYS cc_start: 0.5852 (mttt) cc_final: 0.5321 (tptp) REVERT: A 357 MET cc_start: 0.3963 (tpt) cc_final: 0.2721 (ptm) REVERT: A 388 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6533 (mmtt) REVERT: A 549 MET cc_start: 0.5585 (mmt) cc_final: 0.5337 (mtm) REVERT: A 561 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4388 (mt) REVERT: A 597 LYS cc_start: 0.6136 (ttpt) cc_final: 0.5561 (mmtt) REVERT: A 600 MET cc_start: 0.6730 (tmm) cc_final: 0.5965 (tmm) REVERT: A 633 MET cc_start: 0.5835 (ppp) cc_final: 0.5550 (ppp) REVERT: A 712 ILE cc_start: 0.6574 (mt) cc_final: 0.6372 (mt) REVERT: A 944 MET cc_start: 0.6100 (mmm) cc_final: 0.5730 (mtt) REVERT: A 1044 THR cc_start: 0.6592 (m) cc_final: 0.6248 (p) REVERT: A 1055 ILE cc_start: 0.5968 (mt) cc_final: 0.5654 (mt) REVERT: A 1089 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7388 (mt) REVERT: A 1127 TYR cc_start: 0.5907 (m-10) cc_final: 0.5499 (m-80) REVERT: A 1138 GLU cc_start: 0.6058 (pm20) cc_final: 0.5080 (mm-30) REVERT: A 1170 MET cc_start: 0.6025 (mmm) cc_final: 0.5790 (mmm) REVERT: A 1227 MET cc_start: 0.5286 (mtt) cc_final: 0.5007 (mtp) REVERT: A 1265 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6420 (mt-10) REVERT: A 1439 MET cc_start: 0.2305 (tpt) cc_final: 0.2039 (tpt) REVERT: A 1441 LYS cc_start: 0.6180 (tptt) cc_final: 0.5690 (mmtt) REVERT: A 1487 ASN cc_start: 0.7286 (t0) cc_final: 0.6684 (p0) REVERT: A 1503 HIS cc_start: 0.6888 (t-90) cc_final: 0.6523 (t-90) REVERT: A 1589 MET cc_start: 0.7892 (mmm) cc_final: 0.7378 (mmm) REVERT: A 1592 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7474 (mm-40) REVERT: A 1611 MET cc_start: 0.7295 (ptp) cc_final: 0.6936 (ptt) REVERT: A 1615 TYR cc_start: 0.6817 (t80) cc_final: 0.5875 (t80) REVERT: A 1616 GLU cc_start: 0.6537 (pt0) cc_final: 0.6205 (pt0) REVERT: A 1620 GLN cc_start: 0.7303 (tp40) cc_final: 0.6693 (mp10) REVERT: A 1631 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6507 (ttm110) REVERT: B 153 PHE cc_start: 0.8244 (m-80) cc_final: 0.7853 (m-80) REVERT: B 164 MET cc_start: 0.7429 (ttm) cc_final: 0.7011 (ttm) REVERT: B 268 GLU cc_start: 0.7211 (mp0) cc_final: 0.6759 (mt-10) REVERT: B 372 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7554 (mtp-110) REVERT: B 388 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6608 (tm-30) REVERT: B 408 LEU cc_start: 0.8769 (pp) cc_final: 0.8525 (tp) REVERT: B 623 ASP cc_start: 0.8060 (t0) cc_final: 0.7415 (m-30) REVERT: B 672 MET cc_start: 0.7052 (mmm) cc_final: 0.5992 (ptt) REVERT: B 721 MET cc_start: 0.7250 (tpp) cc_final: 0.7050 (tpp) REVERT: B 723 LYS cc_start: 0.7192 (mttt) cc_final: 0.6920 (mtpt) REVERT: B 726 MET cc_start: 0.6673 (ptt) cc_final: 0.6306 (ptt) REVERT: B 882 ILE cc_start: 0.7222 (mp) cc_final: 0.6633 (mm) REVERT: B 904 LYS cc_start: 0.6688 (ttmm) cc_final: 0.6368 (ttmt) REVERT: B 1082 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6373 (t70) REVERT: B 1097 ASP cc_start: 0.6926 (p0) cc_final: 0.6223 (p0) REVERT: B 1111 LEU cc_start: 0.6684 (mt) cc_final: 0.6202 (pp) REVERT: C 71 MET cc_start: 0.6679 (mtm) cc_final: 0.6212 (mtp) REVERT: C 172 GLN cc_start: 0.6936 (tm-30) cc_final: 0.6474 (tt0) REVERT: E 22 MET cc_start: 0.5711 (ttp) cc_final: 0.5346 (ttt) REVERT: E 93 MET cc_start: 0.4091 (OUTLIER) cc_final: 0.3115 (tmm) REVERT: E 166 LYS cc_start: 0.8231 (tttt) cc_final: 0.7676 (mmtt) REVERT: E 203 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7325 (mt-10) REVERT: F 137 TYR cc_start: 0.5607 (m-80) cc_final: 0.5110 (m-80) REVERT: F 138 LEU cc_start: 0.6643 (mp) cc_final: 0.6378 (mp) REVERT: G 52 MET cc_start: 0.7086 (tmm) cc_final: 0.6676 (tmm) REVERT: G 136 TYR cc_start: 0.3522 (OUTLIER) cc_final: 0.2600 (m-80) REVERT: H 130 ARG cc_start: 0.5064 (ptp-170) cc_final: 0.4525 (ptp-170) REVERT: I 53 ASP cc_start: 0.7674 (p0) cc_final: 0.6560 (t0) REVERT: I 94 MET cc_start: 0.1720 (ttt) cc_final: 0.1358 (ttt) REVERT: K 45 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6543 (mt-10) REVERT: K 110 GLU cc_start: 0.5585 (pt0) cc_final: 0.4904 (tp30) REVERT: K 134 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8246 (tppt) REVERT: N 131 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4805 (mm) REVERT: O 156 MET cc_start: 0.1303 (ptp) cc_final: 0.0972 (mtt) REVERT: O 187 MET cc_start: 0.4724 (mmp) cc_final: 0.3184 (mtt) REVERT: O 396 MET cc_start: 0.6241 (mtp) cc_final: 0.5700 (mtp) REVERT: O 467 MET cc_start: 0.5314 (mmp) cc_final: 0.4827 (mmm) REVERT: O 525 MET cc_start: 0.3051 (ttm) cc_final: 0.2784 (ttm) REVERT: O 608 GLU cc_start: 0.2982 (tm-30) cc_final: 0.2167 (pm20) REVERT: S 305 PHE cc_start: 0.5920 (m-10) cc_final: 0.5574 (t80) REVERT: S 405 TYR cc_start: 0.6689 (t80) cc_final: 0.6363 (t80) REVERT: S 421 ILE cc_start: 0.5375 (tt) cc_final: 0.4932 (tt) REVERT: S 477 TYR cc_start: 0.4742 (t80) cc_final: 0.4435 (t80) REVERT: S 614 GLU cc_start: 0.5289 (mt-10) cc_final: 0.4267 (pp20) REVERT: S 744 LEU cc_start: 0.4960 (tt) cc_final: 0.4211 (mp) REVERT: S 777 MET cc_start: 0.3092 (ppp) cc_final: 0.2681 (tmm) REVERT: R 137 SER cc_start: 0.4301 (p) cc_final: 0.4071 (m) REVERT: R 175 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5784 (mt) REVERT: R 271 LEU cc_start: 0.6579 (mp) cc_final: 0.6226 (tp) REVERT: R 274 MET cc_start: 0.5284 (tpp) cc_final: 0.5048 (tpp) outliers start: 199 outliers final: 120 residues processed: 863 average time/residue: 0.5190 time to fit residues: 759.2162 Evaluate side-chains 704 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 572 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 181 TYR Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1082 HIS Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 150 HIS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 329 ILE Chi-restraints excluded: chain S residue 348 HIS Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 764 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 364 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 351 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 374 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 291 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 462 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 497 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A 880 GLN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 462 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN B 702 ASN B 748 GLN B 912 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 HIS ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN S 232 ASN S 368 HIS R 184 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 1.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52007 Z= 0.215 Angle : 0.709 14.939 70659 Z= 0.362 Chirality : 0.045 0.303 7878 Planarity : 0.005 0.083 8735 Dihedral : 14.277 176.706 7610 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.94 % Allowed : 20.21 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.10), residues: 5986 helix: -1.52 (0.11), residues: 2056 sheet: -1.94 (0.20), residues: 655 loop : -2.07 (0.10), residues: 3275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 314 HIS 0.023 0.001 HIS G 150 PHE 0.053 0.002 PHE B 798 TYR 0.027 0.002 TYR O 602 ARG 0.008 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 654 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3553 (ttp) cc_final: 0.1735 (mmp) REVERT: Q 114 ARG cc_start: 0.6622 (mmp-170) cc_final: 0.6400 (mmm160) REVERT: Q 153 LYS cc_start: 0.5599 (mtpt) cc_final: 0.5289 (mptt) REVERT: Q 177 TYR cc_start: 0.3048 (m-10) cc_final: 0.2828 (m-10) REVERT: Q 190 MET cc_start: 0.8314 (tpp) cc_final: 0.8082 (tmm) REVERT: Q 340 GLN cc_start: 0.5379 (tm-30) cc_final: 0.5000 (tm-30) REVERT: Q 381 MET cc_start: 0.6179 (tpt) cc_final: 0.5937 (tpt) REVERT: Q 488 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5168 (mt) REVERT: M 47 GLU cc_start: -0.2358 (OUTLIER) cc_final: -0.2630 (mt-10) REVERT: M 50 GLU cc_start: 0.6498 (mt-10) cc_final: 0.5170 (pt0) REVERT: M 65 TYR cc_start: 0.5618 (p90) cc_final: 0.5398 (p90) REVERT: M 80 LEU cc_start: 0.5297 (tp) cc_final: 0.4880 (tp) REVERT: A 242 LYS cc_start: 0.0882 (OUTLIER) cc_final: 0.0478 (tttp) REVERT: A 351 LYS cc_start: 0.5116 (mttt) cc_final: 0.4898 (tptp) REVERT: A 357 MET cc_start: 0.3602 (tpt) cc_final: 0.2601 (ptm) REVERT: A 388 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6428 (mptt) REVERT: A 424 MET cc_start: 0.4534 (tmm) cc_final: 0.4041 (tmm) REVERT: A 589 MET cc_start: 0.3970 (ttt) cc_final: 0.3584 (ttt) REVERT: A 600 MET cc_start: 0.6231 (tmm) cc_final: 0.6025 (ttm) REVERT: A 633 MET cc_start: 0.5633 (ppp) cc_final: 0.5217 (ppp) REVERT: A 712 ILE cc_start: 0.6284 (mt) cc_final: 0.6057 (mt) REVERT: A 944 MET cc_start: 0.6115 (mmm) cc_final: 0.5676 (mtt) REVERT: A 1089 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7520 (mt) REVERT: A 1221 ARG cc_start: 0.4519 (tpp-160) cc_final: 0.3436 (tpt90) REVERT: A 1227 MET cc_start: 0.4926 (mtt) cc_final: 0.4692 (mtt) REVERT: A 1250 GLN cc_start: 0.6716 (pt0) cc_final: 0.6344 (pm20) REVERT: A 1265 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6803 (mt-10) REVERT: A 1441 LYS cc_start: 0.6959 (tptt) cc_final: 0.5956 (mmmt) REVERT: A 1485 MET cc_start: 0.5523 (ptp) cc_final: 0.4975 (mtm) REVERT: A 1487 ASN cc_start: 0.7510 (t0) cc_final: 0.6824 (p0) REVERT: A 1503 HIS cc_start: 0.6596 (t-90) cc_final: 0.6182 (t-90) REVERT: A 1572 ARG cc_start: 0.6317 (ttp-110) cc_final: 0.5974 (ptt90) REVERT: A 1592 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7397 (mm-40) REVERT: A 1604 GLU cc_start: 0.4186 (mt-10) cc_final: 0.3149 (tp30) REVERT: A 1611 MET cc_start: 0.7242 (ptp) cc_final: 0.7032 (ptp) REVERT: A 1615 TYR cc_start: 0.6765 (t80) cc_final: 0.5709 (t80) REVERT: A 1620 GLN cc_start: 0.7188 (tp40) cc_final: 0.6663 (mp10) REVERT: A 1631 ARG cc_start: 0.6888 (ttm170) cc_final: 0.6245 (ttm110) REVERT: B 18 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6514 (p) REVERT: B 388 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6450 (tp30) REVERT: B 408 LEU cc_start: 0.8588 (pp) cc_final: 0.8367 (tp) REVERT: B 451 MET cc_start: 0.6385 (tpp) cc_final: 0.4929 (ptm) REVERT: B 623 ASP cc_start: 0.7899 (t0) cc_final: 0.7264 (m-30) REVERT: B 672 MET cc_start: 0.6787 (mmm) cc_final: 0.5308 (ptp) REVERT: B 723 LYS cc_start: 0.7127 (mttt) cc_final: 0.6796 (mtpt) REVERT: B 788 ILE cc_start: 0.7360 (mm) cc_final: 0.7008 (mm) REVERT: B 882 ILE cc_start: 0.6775 (mp) cc_final: 0.6424 (mp) REVERT: B 904 LYS cc_start: 0.6340 (ttmm) cc_final: 0.5972 (ttpt) REVERT: B 940 GLU cc_start: 0.6597 (tm-30) cc_final: 0.6392 (tp30) REVERT: B 1026 ILE cc_start: 0.7808 (mp) cc_final: 0.7522 (mt) REVERT: B 1034 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6178 (mt0) REVERT: B 1097 ASP cc_start: 0.6909 (p0) cc_final: 0.6411 (p0) REVERT: B 1111 LEU cc_start: 0.6357 (mt) cc_final: 0.5804 (pp) REVERT: C 35 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8166 (ptpp) REVERT: C 71 MET cc_start: 0.6049 (mtm) cc_final: 0.5758 (mmm) REVERT: C 172 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6596 (tt0) REVERT: C 283 GLU cc_start: 0.6981 (mp0) cc_final: 0.6740 (mp0) REVERT: C 291 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5893 (tt) REVERT: D 89 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5136 (mt) REVERT: E 22 MET cc_start: 0.5747 (ttp) cc_final: 0.5463 (ttt) REVERT: E 79 TRP cc_start: 0.6749 (t-100) cc_final: 0.6460 (t-100) REVERT: E 93 MET cc_start: 0.3878 (OUTLIER) cc_final: 0.3075 (tmm) REVERT: E 121 MET cc_start: 0.6032 (tpt) cc_final: 0.4724 (mmt) REVERT: E 166 LYS cc_start: 0.8244 (tttt) cc_final: 0.7839 (mmtt) REVERT: F 60 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6131 (mt0) REVERT: F 100 GLN cc_start: 0.5069 (OUTLIER) cc_final: 0.4660 (mt0) REVERT: F 137 TYR cc_start: 0.5552 (m-80) cc_final: 0.5162 (m-80) REVERT: F 138 LEU cc_start: 0.5942 (mp) cc_final: 0.5579 (mp) REVERT: G 136 TYR cc_start: 0.3272 (OUTLIER) cc_final: 0.2390 (m-80) REVERT: G 158 LYS cc_start: 0.6760 (mptt) cc_final: 0.6414 (tptt) REVERT: H 52 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6894 (mp10) REVERT: H 130 ARG cc_start: 0.5361 (ptp-170) cc_final: 0.4320 (ptp-170) REVERT: I 53 ASP cc_start: 0.7736 (p0) cc_final: 0.6690 (t0) REVERT: I 94 MET cc_start: 0.1358 (ttt) cc_final: 0.1035 (ttt) REVERT: K 45 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6576 (mt-10) REVERT: K 110 GLU cc_start: 0.5405 (pt0) cc_final: 0.5077 (tm-30) REVERT: L 62 LYS cc_start: 0.6891 (tmmt) cc_final: 0.6687 (tptp) REVERT: O 180 LEU cc_start: 0.3737 (pp) cc_final: 0.3308 (mt) REVERT: O 187 MET cc_start: 0.4649 (mmp) cc_final: 0.3299 (mtt) REVERT: O 396 MET cc_start: 0.6319 (mtp) cc_final: 0.5567 (mtp) REVERT: O 438 GLN cc_start: 0.5139 (mt0) cc_final: 0.4759 (tt0) REVERT: O 467 MET cc_start: 0.5278 (mmp) cc_final: 0.4663 (mmm) REVERT: O 525 MET cc_start: 0.3202 (ttm) cc_final: 0.2870 (ttm) REVERT: O 608 GLU cc_start: 0.3101 (tm-30) cc_final: 0.2215 (pm20) REVERT: S 300 LEU cc_start: 0.4999 (pt) cc_final: 0.4555 (mp) REVERT: S 305 PHE cc_start: 0.5701 (m-10) cc_final: 0.5355 (t80) REVERT: S 421 ILE cc_start: 0.5095 (tt) cc_final: 0.4631 (tt) REVERT: S 477 TYR cc_start: 0.4626 (t80) cc_final: 0.4127 (t80) REVERT: S 614 GLU cc_start: 0.5174 (mt-10) cc_final: 0.4137 (pp20) REVERT: S 777 MET cc_start: 0.2811 (ppp) cc_final: 0.2272 (tmm) REVERT: R 142 ARG cc_start: 0.4079 (tmm-80) cc_final: 0.2829 (mtt90) REVERT: R 175 ILE cc_start: 0.5785 (OUTLIER) cc_final: 0.5513 (mt) REVERT: R 196 GLU cc_start: 0.5689 (tp30) cc_final: 0.4934 (tm-30) REVERT: R 274 MET cc_start: 0.4839 (tpp) cc_final: 0.4169 (tpt) REVERT: R 308 PHE cc_start: 0.4900 (p90) cc_final: 0.4309 (p90) outliers start: 161 outliers final: 91 residues processed: 772 average time/residue: 0.5102 time to fit residues: 663.9368 Evaluate side-chains 672 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 567 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 41 PHE Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 150 HIS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 348 HIS Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 500 ILE Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 535 optimal weight: 9.9990 chunk 564 optimal weight: 0.9980 chunk 514 optimal weight: 0.9990 chunk 548 optimal weight: 20.0000 chunk 330 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 430 optimal weight: 0.0980 chunk 168 optimal weight: 1.9990 chunk 495 optimal weight: 0.9980 chunk 519 optimal weight: 7.9990 chunk 546 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A 880 GLN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B 912 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 HIS ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 297 HIS ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 1.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 52007 Z= 0.208 Angle : 0.686 14.273 70659 Z= 0.351 Chirality : 0.045 0.305 7878 Planarity : 0.005 0.084 8735 Dihedral : 14.160 177.582 7610 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.30 % Favored : 92.68 % Rotamer: Outliers : 2.25 % Allowed : 21.33 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.10), residues: 5986 helix: -1.28 (0.11), residues: 2050 sheet: -1.91 (0.20), residues: 638 loop : -2.00 (0.10), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 314 HIS 0.033 0.001 HIS G 150 PHE 0.044 0.002 PHE B 798 TYR 0.022 0.002 TYR J 21 ARG 0.011 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 614 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3538 (ttp) cc_final: 0.1641 (mmp) REVERT: Q 114 ARG cc_start: 0.6613 (mmp-170) cc_final: 0.6398 (mmm160) REVERT: Q 153 LYS cc_start: 0.5601 (mtpt) cc_final: 0.5235 (mptt) REVERT: Q 158 MET cc_start: 0.2197 (ttp) cc_final: 0.1901 (ttp) REVERT: Q 183 LYS cc_start: 0.4754 (ttpp) cc_final: 0.4114 (mttt) REVERT: Q 340 GLN cc_start: 0.5449 (tm-30) cc_final: 0.5054 (tm-30) REVERT: Q 381 MET cc_start: 0.6221 (tpt) cc_final: 0.5948 (tpt) REVERT: Q 488 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5298 (mt) REVERT: M 47 GLU cc_start: -0.1971 (OUTLIER) cc_final: -0.2271 (mt-10) REVERT: M 65 TYR cc_start: 0.5629 (p90) cc_final: 0.5414 (p90) REVERT: M 80 LEU cc_start: 0.5514 (tp) cc_final: 0.5000 (tp) REVERT: A 70 LYS cc_start: 0.2873 (mtmt) cc_final: 0.2443 (ptpp) REVERT: A 242 LYS cc_start: 0.1052 (OUTLIER) cc_final: 0.0611 (tttp) REVERT: A 357 MET cc_start: 0.3845 (tpt) cc_final: 0.2760 (ptt) REVERT: A 388 LYS cc_start: 0.6915 (ttmp) cc_final: 0.6470 (mmtt) REVERT: A 424 MET cc_start: 0.4064 (tmm) cc_final: 0.3624 (tmm) REVERT: A 470 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5107 (t-90) REVERT: A 549 MET cc_start: 0.5023 (mmt) cc_final: 0.4728 (mtt) REVERT: A 589 MET cc_start: 0.4216 (ttt) cc_final: 0.3811 (ttt) REVERT: A 633 MET cc_start: 0.5690 (ppp) cc_final: 0.5342 (ppp) REVERT: A 944 MET cc_start: 0.6164 (mmm) cc_final: 0.5892 (mtt) REVERT: A 964 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8190 (ptmt) REVERT: A 1023 LEU cc_start: 0.6119 (tp) cc_final: 0.5902 (tp) REVERT: A 1089 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7544 (mt) REVERT: A 1221 ARG cc_start: 0.4415 (tpp-160) cc_final: 0.3841 (tmt-80) REVERT: A 1227 MET cc_start: 0.4965 (mtt) cc_final: 0.4714 (mtt) REVERT: A 1250 GLN cc_start: 0.6524 (pt0) cc_final: 0.6154 (pm20) REVERT: A 1439 MET cc_start: 0.2521 (tpp) cc_final: 0.2180 (mmm) REVERT: A 1485 MET cc_start: 0.5249 (ptp) cc_final: 0.4363 (mtm) REVERT: A 1487 ASN cc_start: 0.7551 (t0) cc_final: 0.6889 (p0) REVERT: A 1503 HIS cc_start: 0.6467 (t-90) cc_final: 0.6015 (t-90) REVERT: A 1589 MET cc_start: 0.7896 (mmm) cc_final: 0.7448 (mmm) REVERT: A 1604 GLU cc_start: 0.4084 (mt-10) cc_final: 0.3329 (tp30) REVERT: A 1611 MET cc_start: 0.7399 (ptp) cc_final: 0.7194 (ptp) REVERT: A 1615 TYR cc_start: 0.6810 (t80) cc_final: 0.5704 (t80) REVERT: A 1620 GLN cc_start: 0.7048 (tp40) cc_final: 0.6573 (mp10) REVERT: A 1631 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6212 (mtp-110) REVERT: B 164 MET cc_start: 0.7097 (ttm) cc_final: 0.6872 (ttm) REVERT: B 388 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6703 (tm-30) REVERT: B 408 LEU cc_start: 0.8513 (pp) cc_final: 0.8246 (tp) REVERT: B 451 MET cc_start: 0.6124 (tpp) cc_final: 0.4656 (ptp) REVERT: B 623 ASP cc_start: 0.7795 (t0) cc_final: 0.7287 (m-30) REVERT: B 672 MET cc_start: 0.6930 (mmm) cc_final: 0.5556 (ptt) REVERT: B 723 LYS cc_start: 0.7128 (mttt) cc_final: 0.6803 (mtpt) REVERT: B 788 ILE cc_start: 0.7382 (mm) cc_final: 0.6970 (mm) REVERT: B 882 ILE cc_start: 0.6489 (mp) cc_final: 0.6117 (mp) REVERT: B 904 LYS cc_start: 0.6523 (ttmm) cc_final: 0.6165 (ttpt) REVERT: B 957 ARG cc_start: 0.5395 (mpt180) cc_final: 0.4977 (mtp180) REVERT: B 1013 MET cc_start: 0.6403 (ptt) cc_final: 0.5948 (ptt) REVERT: B 1026 ILE cc_start: 0.7784 (mp) cc_final: 0.7443 (mp) REVERT: B 1034 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6215 (mt0) REVERT: B 1097 ASP cc_start: 0.6939 (p0) cc_final: 0.6522 (p0) REVERT: B 1111 LEU cc_start: 0.6528 (mt) cc_final: 0.6009 (pp) REVERT: C 35 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8109 (ptpp) REVERT: C 172 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6622 (tt0) REVERT: C 283 GLU cc_start: 0.6997 (mp0) cc_final: 0.6782 (mp0) REVERT: C 291 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6100 (tt) REVERT: D 89 LEU cc_start: 0.5477 (OUTLIER) cc_final: 0.5090 (mp) REVERT: E 22 MET cc_start: 0.5513 (ttp) cc_final: 0.5255 (ttt) REVERT: E 40 GLU cc_start: 0.7969 (pm20) cc_final: 0.7421 (pm20) REVERT: E 58 MET cc_start: 0.7206 (pmm) cc_final: 0.6967 (pmm) REVERT: E 93 MET cc_start: 0.4031 (OUTLIER) cc_final: 0.3280 (tmm) REVERT: E 121 MET cc_start: 0.6099 (tpt) cc_final: 0.4745 (mmt) REVERT: E 166 LYS cc_start: 0.8114 (tttt) cc_final: 0.7781 (mmtt) REVERT: F 60 GLN cc_start: 0.6855 (mm-40) cc_final: 0.6010 (mt0) REVERT: F 100 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4277 (mt0) REVERT: F 137 TYR cc_start: 0.5577 (m-80) cc_final: 0.5278 (m-80) REVERT: F 138 LEU cc_start: 0.5594 (mp) cc_final: 0.5221 (mp) REVERT: F 154 ASP cc_start: 0.3686 (m-30) cc_final: 0.2755 (p0) REVERT: G 72 LYS cc_start: 0.6706 (mttt) cc_final: 0.6092 (pttp) REVERT: G 94 PRO cc_start: 0.5866 (Cg_exo) cc_final: 0.5538 (Cg_endo) REVERT: G 136 TYR cc_start: 0.3451 (OUTLIER) cc_final: 0.2591 (m-80) REVERT: H 130 ARG cc_start: 0.5088 (ptp-170) cc_final: 0.4164 (ptp-170) REVERT: I 53 ASP cc_start: 0.7757 (p0) cc_final: 0.6766 (t0) REVERT: J 2 ILE cc_start: 0.8834 (mt) cc_final: 0.8545 (mt) REVERT: K 45 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6728 (mt-10) REVERT: K 110 GLU cc_start: 0.5427 (pt0) cc_final: 0.4807 (tm-30) REVERT: L 42 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: L 62 LYS cc_start: 0.6772 (tmmt) cc_final: 0.6494 (tppt) REVERT: N 162 LYS cc_start: 0.6515 (tppt) cc_final: 0.6269 (tmtt) REVERT: N 169 GLU cc_start: 0.5478 (OUTLIER) cc_final: 0.4059 (pt0) REVERT: O 128 LEU cc_start: 0.3598 (mt) cc_final: 0.2708 (pt) REVERT: O 156 MET cc_start: 0.1127 (mtt) cc_final: 0.0510 (ptp) REVERT: O 180 LEU cc_start: 0.4184 (pp) cc_final: 0.3675 (mt) REVERT: O 187 MET cc_start: 0.4783 (mmp) cc_final: 0.3508 (mtt) REVERT: O 396 MET cc_start: 0.6223 (mtp) cc_final: 0.5409 (mtp) REVERT: O 438 GLN cc_start: 0.5146 (mt0) cc_final: 0.4689 (tt0) REVERT: O 467 MET cc_start: 0.5383 (mmp) cc_final: 0.4729 (mmm) REVERT: O 525 MET cc_start: 0.3180 (ttm) cc_final: 0.2845 (ttm) REVERT: O 602 TYR cc_start: 0.4355 (t80) cc_final: 0.3802 (t80) REVERT: O 608 GLU cc_start: 0.3304 (tm-30) cc_final: 0.2376 (pm20) REVERT: S 300 LEU cc_start: 0.5004 (pt) cc_final: 0.4589 (mp) REVERT: S 305 PHE cc_start: 0.5538 (m-10) cc_final: 0.5241 (t80) REVERT: S 614 GLU cc_start: 0.5318 (mt-10) cc_final: 0.4132 (pp20) REVERT: S 744 LEU cc_start: 0.4094 (tt) cc_final: 0.3323 (mp) REVERT: S 777 MET cc_start: 0.2937 (ppp) cc_final: 0.2371 (tmm) REVERT: R 16 ARG cc_start: 0.7264 (ptp-110) cc_final: 0.6991 (mtm180) REVERT: R 142 ARG cc_start: 0.4027 (tmm-80) cc_final: 0.2691 (mtt90) REVERT: R 175 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.5354 (mt) REVERT: R 196 GLU cc_start: 0.5692 (tp30) cc_final: 0.4999 (tm-30) REVERT: R 274 MET cc_start: 0.4991 (tpp) cc_final: 0.4613 (tpt) outliers start: 123 outliers final: 82 residues processed: 703 average time/residue: 0.5022 time to fit residues: 597.2944 Evaluate side-chains 669 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 572 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 41 PHE Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1034 GLN Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 150 HIS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 488 LEU Chi-restraints excluded: chain S residue 536 ASP Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 704 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 360 optimal weight: 0.0970 chunk 580 optimal weight: 9.9990 chunk 354 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 403 optimal weight: 10.0000 chunk 608 optimal weight: 9.9990 chunk 560 optimal weight: 1.9990 chunk 484 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 374 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 322 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 282 HIS ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B 912 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS B1082 HIS ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS D 29 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 370 GLN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 1.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 52007 Z= 0.194 Angle : 0.672 14.520 70659 Z= 0.342 Chirality : 0.044 0.308 7878 Planarity : 0.005 0.085 8735 Dihedral : 14.057 178.056 7610 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.53 % Favored : 93.45 % Rotamer: Outliers : 2.09 % Allowed : 21.64 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 5986 helix: -1.13 (0.11), residues: 2069 sheet: -1.69 (0.21), residues: 616 loop : -1.93 (0.10), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 314 HIS 0.067 0.001 HIS G 150 PHE 0.034 0.002 PHE B 313 TYR 0.020 0.001 TYR J 21 ARG 0.009 0.001 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 614 time to evaluate : 4.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3532 (ttp) cc_final: 0.1651 (mmp) REVERT: Q 109 GLN cc_start: 0.7778 (pp30) cc_final: 0.6460 (tt0) REVERT: Q 114 ARG cc_start: 0.6726 (mmp-170) cc_final: 0.6337 (mmm160) REVERT: Q 153 LYS cc_start: 0.5444 (mtpt) cc_final: 0.5090 (mptt) REVERT: Q 158 MET cc_start: 0.2594 (ttp) cc_final: 0.2244 (ttp) REVERT: Q 183 LYS cc_start: 0.4779 (ttpp) cc_final: 0.4230 (mttt) REVERT: Q 340 GLN cc_start: 0.5305 (tm-30) cc_final: 0.4905 (tm-30) REVERT: Q 381 MET cc_start: 0.6042 (tpt) cc_final: 0.5783 (tpt) REVERT: Q 488 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5287 (mt) REVERT: M 80 LEU cc_start: 0.5550 (tp) cc_final: 0.5028 (tp) REVERT: A 70 LYS cc_start: 0.3259 (mtmt) cc_final: 0.2790 (ptpp) REVERT: A 357 MET cc_start: 0.3923 (tpt) cc_final: 0.2983 (ptm) REVERT: A 388 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6520 (mptt) REVERT: A 424 MET cc_start: 0.4044 (tmm) cc_final: 0.3595 (tmm) REVERT: A 470 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5175 (t-90) REVERT: A 549 MET cc_start: 0.4946 (mmt) cc_final: 0.4675 (mtt) REVERT: A 589 MET cc_start: 0.4287 (ttt) cc_final: 0.3754 (ttt) REVERT: A 633 MET cc_start: 0.5640 (ppp) cc_final: 0.5289 (ppp) REVERT: A 944 MET cc_start: 0.6166 (mmm) cc_final: 0.5848 (mtt) REVERT: A 964 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8225 (ptmt) REVERT: A 1089 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 1221 ARG cc_start: 0.4575 (tpp-160) cc_final: 0.4101 (tmt-80) REVERT: A 1227 MET cc_start: 0.4838 (mtt) cc_final: 0.4581 (mtt) REVERT: A 1250 GLN cc_start: 0.6361 (pt0) cc_final: 0.6012 (pm20) REVERT: A 1439 MET cc_start: 0.3118 (tpp) cc_final: 0.2735 (mmm) REVERT: A 1441 LYS cc_start: 0.6655 (tptt) cc_final: 0.5240 (mmmt) REVERT: A 1485 MET cc_start: 0.5113 (ptp) cc_final: 0.4311 (mtm) REVERT: A 1487 ASN cc_start: 0.7631 (t0) cc_final: 0.6970 (p0) REVERT: A 1503 HIS cc_start: 0.6435 (t-90) cc_final: 0.5992 (t-90) REVERT: A 1589 MET cc_start: 0.7863 (mmm) cc_final: 0.7330 (mmm) REVERT: A 1604 GLU cc_start: 0.4894 (mt-10) cc_final: 0.4168 (tp30) REVERT: A 1615 TYR cc_start: 0.6777 (t80) cc_final: 0.5669 (t80) REVERT: A 1620 GLN cc_start: 0.7049 (tp40) cc_final: 0.6503 (mp10) REVERT: A 1631 ARG cc_start: 0.6938 (ttm170) cc_final: 0.6178 (mtp-110) REVERT: B 18 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6597 (p) REVERT: B 175 MET cc_start: 0.5334 (ttt) cc_final: 0.4875 (ttt) REVERT: B 316 ARG cc_start: 0.5546 (tpt90) cc_final: 0.4601 (ptp-170) REVERT: B 388 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6712 (tm-30) REVERT: B 408 LEU cc_start: 0.8518 (pp) cc_final: 0.8233 (tp) REVERT: B 451 MET cc_start: 0.6116 (tpp) cc_final: 0.4711 (ptm) REVERT: B 672 MET cc_start: 0.6804 (mmm) cc_final: 0.5896 (ptt) REVERT: B 723 LYS cc_start: 0.7087 (mttt) cc_final: 0.6812 (mtpt) REVERT: B 788 ILE cc_start: 0.7327 (mm) cc_final: 0.6983 (mm) REVERT: B 839 LYS cc_start: 0.6697 (mmtt) cc_final: 0.6469 (ttmm) REVERT: B 904 LYS cc_start: 0.6424 (ttmm) cc_final: 0.6084 (ttpt) REVERT: B 957 ARG cc_start: 0.5356 (mpt180) cc_final: 0.4948 (mtp180) REVERT: B 1013 MET cc_start: 0.6579 (ptt) cc_final: 0.6080 (ptt) REVERT: B 1026 ILE cc_start: 0.7820 (mp) cc_final: 0.7471 (mp) REVERT: B 1097 ASP cc_start: 0.6806 (p0) cc_final: 0.6402 (p0) REVERT: B 1099 THR cc_start: 0.7492 (p) cc_final: 0.7278 (p) REVERT: B 1111 LEU cc_start: 0.6586 (mt) cc_final: 0.6070 (pp) REVERT: C 172 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6307 (tt0) REVERT: C 291 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6256 (tt) REVERT: D 47 LYS cc_start: 0.5053 (mmtt) cc_final: 0.4798 (tmtt) REVERT: D 89 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5369 (mt) REVERT: E 22 MET cc_start: 0.5570 (ttp) cc_final: 0.5340 (ttt) REVERT: E 93 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.3169 (tmm) REVERT: E 121 MET cc_start: 0.6051 (tpt) cc_final: 0.4810 (mmt) REVERT: E 166 LYS cc_start: 0.8093 (tttt) cc_final: 0.7743 (mmtt) REVERT: F 60 GLN cc_start: 0.6564 (mm-40) cc_final: 0.5727 (mt0) REVERT: F 100 GLN cc_start: 0.5132 (OUTLIER) cc_final: 0.4376 (mt0) REVERT: F 137 TYR cc_start: 0.5488 (m-80) cc_final: 0.5208 (m-80) REVERT: F 138 LEU cc_start: 0.5816 (mp) cc_final: 0.5479 (mp) REVERT: F 154 ASP cc_start: 0.3839 (m-30) cc_final: 0.2838 (p0) REVERT: G 72 LYS cc_start: 0.6703 (mttt) cc_final: 0.6105 (pttp) REVERT: G 94 PRO cc_start: 0.5304 (Cg_exo) cc_final: 0.4970 (Cg_endo) REVERT: G 136 TYR cc_start: 0.3826 (OUTLIER) cc_final: 0.3031 (m-80) REVERT: H 130 ARG cc_start: 0.5007 (ptp-170) cc_final: 0.4248 (ptp-170) REVERT: I 53 ASP cc_start: 0.7567 (p0) cc_final: 0.6715 (t0) REVERT: J 2 ILE cc_start: 0.8972 (mt) cc_final: 0.8643 (mt) REVERT: K 45 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6755 (mt-10) REVERT: K 110 GLU cc_start: 0.5431 (pt0) cc_final: 0.4854 (tm-30) REVERT: L 66 GLN cc_start: 0.5171 (OUTLIER) cc_final: 0.4932 (mp10) REVERT: N 107 MET cc_start: 0.4975 (mmp) cc_final: 0.4278 (mmt) REVERT: N 169 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.3789 (pt0) REVERT: O 128 LEU cc_start: 0.3321 (mt) cc_final: 0.2620 (pt) REVERT: O 156 MET cc_start: 0.1102 (mtt) cc_final: 0.0576 (ptp) REVERT: O 167 LYS cc_start: 0.2021 (ptmt) cc_final: 0.1775 (mmmt) REVERT: O 180 LEU cc_start: 0.4667 (pp) cc_final: 0.4131 (mt) REVERT: O 187 MET cc_start: 0.4867 (mmp) cc_final: 0.3491 (mtt) REVERT: O 396 MET cc_start: 0.6569 (mtp) cc_final: 0.5915 (mpp) REVERT: O 438 GLN cc_start: 0.5342 (mt0) cc_final: 0.4928 (tt0) REVERT: O 467 MET cc_start: 0.5547 (mmp) cc_final: 0.4914 (mmm) REVERT: O 525 MET cc_start: 0.3178 (ttm) cc_final: 0.2840 (ttm) REVERT: O 608 GLU cc_start: 0.3342 (tm-30) cc_final: 0.2397 (pm20) REVERT: S 300 LEU cc_start: 0.5019 (pt) cc_final: 0.4642 (mp) REVERT: S 305 PHE cc_start: 0.5724 (m-10) cc_final: 0.5305 (t80) REVERT: S 386 MET cc_start: 0.4063 (OUTLIER) cc_final: 0.3838 (pmm) REVERT: S 614 GLU cc_start: 0.5445 (mt-10) cc_final: 0.4237 (pp20) REVERT: S 744 LEU cc_start: 0.4193 (tt) cc_final: 0.3235 (mp) REVERT: S 777 MET cc_start: 0.3153 (ppp) cc_final: 0.2499 (tmm) REVERT: R 142 ARG cc_start: 0.4014 (tmm-80) cc_final: 0.2637 (mtt90) REVERT: R 175 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.5422 (mt) REVERT: R 196 GLU cc_start: 0.5773 (tp30) cc_final: 0.5141 (tm-30) REVERT: R 274 MET cc_start: 0.5209 (tpp) cc_final: 0.4968 (tpt) outliers start: 114 outliers final: 76 residues processed: 698 average time/residue: 0.5135 time to fit residues: 604.9123 Evaluate side-chains 651 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 560 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 41 PHE Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 488 LEU Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 370 GLN Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 488 LEU Chi-restraints excluded: chain S residue 536 ASP Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 704 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 385 optimal weight: 10.0000 chunk 516 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 446 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 485 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 498 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A1141 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 297 HIS ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 ASN S 348 HIS S 368 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.216192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.192586 restraints weight = 77253.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.192166 restraints weight = 103137.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.193128 restraints weight = 97598.045| |-----------------------------------------------------------------------------| r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4697 r_free = 0.4697 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 666 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4697 r_free = 0.4697 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 667 | |-----------------------------------------------------------------------------| r_final: 0.4697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 1.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 52007 Z= 0.275 Angle : 0.733 14.061 70659 Z= 0.376 Chirality : 0.047 0.335 7878 Planarity : 0.005 0.080 8735 Dihedral : 14.178 179.243 7610 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.25 % Allowed : 21.77 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.10), residues: 5986 helix: -1.26 (0.11), residues: 2058 sheet: -1.82 (0.20), residues: 644 loop : -2.00 (0.10), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP Q 118 HIS 0.022 0.002 HIS S 368 PHE 0.046 0.002 PHE S 369 TYR 0.028 0.002 TYR J 21 ARG 0.012 0.001 ARG E 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11827.96 seconds wall clock time: 205 minutes 43.90 seconds (12343.90 seconds total)